Restoring backup files from Time Machine without system preference/Library files

Hi all. I recently ran into some trouble with my MBP and had the Apple store do a erase/install for me. At the time when I got my laptop back, I was told it would be best if I transferred my files including applications the drag and drop way to avoid restoring library/system files that could've been the cause of the problem in the first place. I'm currently still at the setup assistant stage and I'm really unsure of what to do to be honest because I'm under the impression that my application settings would pretty much be gone if I did the drag and drop method.
I read that setup assistant transfers only files that you want but I also read something from user Pondini that the Library files are automatically restored even if I unchecked everything. Which is problematic since that's what I want to avoid in the first place. If possible can anyone recommend a better option for my dilemma? I've read in one of the forum boards that dragging and dropping files can also cause some problems with how applications will work and I really don't want to have to deal with that after the trouble I'm going through with this. Is there a way to just restore Applications and the user folder (desktop, documents, downloads, etc) without including the library system files and folders through setup assistant?
Or do I really have to deal with dragging and dropping files instead? Would you recommend doing the stars wars method of Time Machine and picking only the files I want? Would that be most advisable?
Also, it would be really helpful if anyone can explain to me what the "other files and folders" mean exactly. Thanks very much!

Well what happened was my laptop ran into 2 kernel panics within 2 days (I posted a question here: https://discussions.apple.com/message/25605663#25605663). Which sent ME into a panic. I couldn't trust myself to go any further so I went to the Apple store who then helped did an erase/install for me because they suspect it could be a software issue (maybe it was missing codes or something) and suggested that it would be best for me to drag/drop restore my stuff manually. I'm not very keen on a full system restore either because I know there are some system files which I'd rather not have sticking around (like com.rims which are super stubborn to get rid of) and which could even have been the source of my trouble right now.
I was reading through every single page of Pondini's articles and I'm couldn't find anything which said I could just restore the apps in my apps folder without transferring anything else (ie. the library folder in the macintosh hd folder) since i'm assuming anything from the library folder of the user would be obsolete if I choose not to restore those files using setup assistant. But I'm more reluctant about not using setup assistant for restoring my apps because I don't know how bad it will turn out. Not to mention I won't know if they would restore system root files that should've been long gone since I uninstalled them.

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    6/11/14 3:16:35.000 PM kernel[0]: disk1s2: I/O error.
    6/11/14 3:16:50.710 PM com.apple.backupd-helper[533]: Not starting scheduled Time Machine backup: Backup already running
    6/11/14 3:16:53.000 PM kernel[0]: disk1s2: I/O error.
    6/11/14 3:17:00.000 PM kernel[0]: disk1s2: I/O error.
    6/11/14 3:17:00.552 PM com.apple.backupd[532]: Error: (-36) SrcErr:YES Copying /Volumes/Media/itunes Media/Mobile Applications/Archetype 1.6.2.ipa to (null)
    6/11/14 3:17:10.000 PM kernel[0]: disk1s2: I/O error.
    6/11/14 3:17:23.000 PM kernel[0]: disk1s2: I/O error.
    6/11/14 3:17:35.000 PM kernel[0]: disk1s2: I/O error.
    6/11/14 3:17:49.000 PM kernel[0]: disk1s2: I/O error.
    6/11/14 3:18:01.000 PM kernel[0]: disk1s2: I/O error.
    6/11/14 3:18:14.000 PM kernel[0]: disk1s2: I/O error.
    6/11/14 3:18:28.000 PM kernel[0]: disk1s2: I/O error.
    6/11/14 3:18:40.000 PM kernel[0]: disk1s2: I/O error.
    6/11/14 3:19:03.000 PM kernel[0]: disk1s2: I/O error.
    6/11/14 3:19:06.000 PM kernel[0]: disk1s2: I/O error.
    6/11/14 3:19:18.000 PM kernel[0]: disk1s2: I/O error.
    6/11/14 3:19:41.000 PM kernel[0]: disk1s2: I/O error.
    6/11/14 3:19:43.000 PM kernel[0]: disk1s2: I/O error.
    6/11/14 3:19:56.000 PM kernel[0]: disk1s2: I/O error.
    6/11/14 3:20:11.000 PM kernel[0]: disk1s2: I/O error.
    6/11/14 3:20:23.000 PM kernel[0]: disk1s2: I/O error.
    6/11/14 3:20:36.000 PM kernel[0]: disk1s2: I/O error.
    6/11/14 3:20:48.000 PM kernel[0]: disk1s2: I/O error.
    6/11/14 3:21:01.000 PM kernel[0]: disk1s2: I/O error.
    6/11/14 3:21:13.000 PM kernel[0]: disk1s2: I/O error.
    6/11/14 3:21:26.000 PM kernel[0]: disk1s2: I/O error.
    6/11/14 3:21:38.000 PM kernel[0]: disk1s2: I/O error.
    6/11/14 3:21:51.000 PM kernel[0]: disk1s2: I/O error.
    6/11/14 3:22:03.000 PM kernel[0]: disk1s2: I/O error.
    6/11/14 3:22:16.000 PM kernel[0]: disk1s2: I/O error.
    6/11/14 3:22:28.000 PM kernel[0]: disk1s2: I/O error.
    6/11/14 3:22:41.000 PM kernel[0]: disk1s2: I/O error.
    6/11/14 3:22:53.000 PM kernel[0]: disk1s2: I/O error.
    6/11/14 3:23:06.000 PM kernel[0]: disk1s2: I/O error.
    6/11/14 3:23:19.000 PM kernel[0]: disk1s2: I/O error.
    6/11/14 3:23:31.000 PM kernel[0]: disk1s2: I/O error.
    6/11/14 3:23:57.000 PM kernel[0]: disk1s2: I/O error.
    6/11/14 3:24:09.000 PM kernel[0]: disk1s2: I/O error.
    6/11/14 3:24:22.000 PM kernel[0]: disk1s2: I/O error.
    6/11/14 3:24:38.000 PM kernel[0]: disk1s2: I/O error.
    6/11/14 3:24:50.000 PM kernel[0]: disk1s2: I/O error.
    6/11/14 3:25:03.000 PM kernel[0]: disk1s2: I/O error.
    6/11/14 3:25:15.000 PM kernel[0]: disk1s2: I/O error.
    6/11/14 3:25:35.000 PM kernel[0]: disk1s2: I/O error.
    6/11/14 3:25:47.000 PM kernel[0]: disk1s2: I/O error.
    6/11/14 3:25:47.887 PM com.apple.backupd[532]: Error: (-36) SrcErr:YES Copying /Volumes/Media/itunes Media/Mobile Applications/Bloomberg 3.0.ipa to (null)
    6/11/14 3:26:01.000 PM kernel[0]: disk1s2: I/O error.
    6/11/14 3:26:13.000 PM kernel[0]: disk1s2: I/O error.
    6/11/14 3:26:13.942 PM com.apple.backupd[532]: Error: (-36) SrcErr:YES Copying /Volumes/Media/itunes Media/Mobile Applications/Calculator 3.4.ipa to (null)
    6/11/14 3:26:26.000 PM kernel[0]: disk1s2: I/O error.
    6/11/14 3:26:26.509 PM com.apple.backupd[532]: Error: (-36) SrcErr:YES Copying /Volumes/Media/itunes Media/Mobile Applications/Camera Zoom 3.1.ipa to (null)
    6/11/14 3:26:39.000 PM kernel[0]: disk1s2: I/O error.
    6/11/14 3:26:52.000 PM kernel[0]: disk1s2: I/O error.
    6/11/14 3:26:52.108 PM com.apple.backupd[532]: Error: (-36) SrcErr:YES Copying /Volumes/Media/itunes Media/Mobile Applications/Cards 2.0.1.ipa to (null)
    6/11/14 3:27:14.000 PM kernel[0]: disk1s2: I/O error.
    6/11/14 3:27:17.000 PM kernel[0]: disk1s2: I/O error.
    6/11/14 3:27:29.000 PM kernel[0]: disk1s2: I/O error.
    6/11/14 3:27:29.606 PM com.apple.backupd[532]: Error: (-36) SrcErr:YES Copying /Volumes/Media/itunes Media/Mobile Applications/Casino 2.5.ipa to (null)
    6/11/14 3:27:47.000 PM kernel[0]: disk1s2: I/O error.
    6/11/14 3:28:00.000 PM kernel[0]: disk1s2: I/O error.
    6/11/14 3:28:00.327 PM com.apple.backupd[532]: Error: (-36) SrcErr:YES Copying /Volumes/Media/itunes Media/Mobile Applications/Clear Day 2.6.ipa to (null)
    6/11/14 3:28:14.000 PM kernel[0]: disk1s2: I/O error.
    6/11/14 3:28:26.000 PM kernel[0]: disk1s2: I/O error.
    6/11/14 3:28:39.000 PM kernel[0]: disk1s2: I/O error.
    6/11/14 3:28:56.000 PM kernel[0]: disk1s2: I/O error.
    6/11/14 3:29:09.000 PM kernel[0]: disk1s2: I/O error.
    6/11/14 3:29:21.000 PM kernel[0]: disk1s2: I/O error.
    6/11/14 3:29:34.000 PM kernel[0]: disk1s2: I/O error.
    6/11/14 3:29:47.000 PM kernel[0]: disk1s2: I/O error.
    6/11/14 3:29:59.000 PM kernel[0]: disk1s2: I/O error.
    6/11/14 3:30:12.000 PM kernel[0]: disk1s2: I/O error.
    6/11/14 3:30:24.000 PM kernel[0]: disk1s2: I/O error.
    6/11/14 3:30:37.000 PM kernel[0]: disk1s2: I/O error.
    6/11/14 3:30:49.085 PM xpcproxy[629]: assertion failed: 13D65: xpcproxy + 3438 [D559FC96-E6B1-363A-B850-C7AC9734F210]: 0x2
    6/11/14 3:30:49.000 PM kernel[0]: disk1s2: I/O error.
    6/11/14 3:30:50.194 PM syncdefaultsd[628]: Fixing push token
    6/11/14 3:30:52.507 PM xpcproxy[632]: assertion failed: 13D65: xpcproxy + 3438 [D559FC96-E6B1-363A-B850-C7AC9734F210]: 0x2
    6/11/14 3:31:02.000 PM kernel[0]: disk1s2: I/O error.
    6/11/14 3:31:14.000 PM kernel[0]: disk1s2: I/O error.
    6/11/14 3:31:27.000 PM kernel[0]: disk1s2: I/O error.
    6/11/14 3:31:39.000 PM kernel[0]: disk1s2: I/O error.
    6/11/14 3:31:52.000 PM kernel[0]: disk1s2: I/O error.
    6/11/14 3:32:05.000 PM kernel[0]: disk1s2: I/O error.
    6/11/14 3:32:17.000 PM kernel[0]: disk1s2: I/O error.
    6/11/14 3:32:30.000 PM kernel[0]: disk1s2: I/O error.
    6/11/14 3:32:42.000 PM kernel[0]: disk1s2: I/O error.
    6/11/14 3:32:55.000 PM kernel[0]: disk1s2: I/O error.
    6/11/14 3:33:07.000 PM kernel[0]: disk1s2: I/O error.
    6/11/14 3:33:30.000 PM kernel[0]: disk1s2: I/O error.
    6/11/14 3:33:32.000 PM kernel[0]: disk1s2: I/O error.
    6/11/14 3:33:55.000 PM kernel[0]: disk1s2: I/O error.
    6/11/14 3:33:58.000 PM kernel[0]: disk1s2: I/O error.
    6/11/14 3:34:21.000 PM kernel[0]: disk1s2: I/O error.
    6/11/14 3:34:23.000 PM kernel[0]: disk1s2: I/O error.
    6/11/14 3:34:46.000 PM kernel[0]: disk1s2: I/O error.
    6/11/14 3:34:49.000 PM kernel[0]: disk1s2: I/O error.
    6/11/14 3:35:02.000 PM kernel[0]: disk1s2: I/O error.
    6/11/14 3:35:18.000 PM kernel[0]: disk1s2: I/O error.
    6/11/14 3:35:30.000 PM kernel[0]: disk1s2: I/O error.
    6/11/14 3:35:30.676 PM com.apple.backupd[532]: Error: (-36) SrcErr:YES Copying /Volumes/Media/itunes Media/Mobile Applications/Collection HD 1.7.ipa to (null)
    6/11/14 3:36:14.000 PM kernel[0]: disk1s2: I/O error.
    6/11/14 3:36:17.000 PM kernel[0]: disk1s2: I/O error.
    6/11/14 3:36:29.000 PM kernel[0]: disk1s2: I/O error.
    6/11/14 3:36:29.651 PM com.apple.backupd[532]: Error: (-36) SrcErr:YES Copying /Volumes/Media/itunes Media/Mobile Applications/eCardExpress 2.1.ipa to (null)
    6/11/14 3:36:52.000 PM kernel[0]: disk1s2: I/O error.
    6/11/14 3:37:14.000 PM kernel[0]: disk1s2: I/O error.
    6/11/14 3:37:17.000 PM kernel[0]: disk1s2: I/O error.
    6/11/14 3:37:30.000 PM kernel[0]: disk1s2: I/O error.
    6/11/14 3:37:52.000 PM kernel[0]: disk1s2: I/O error.
    6/11/14 3:37:55.000 PM kernel[0]: disk1s2: I/O error.
    6/11/14 3:38:07.000 PM kernel[0]: disk1s2: I/O error.
    6/11/14 3:38:30.000 PM kernel[0]: disk1s2: I/O error.
    6/11/14 3:38:32.000 PM kernel[0]: disk1s2: I/O error.
    6/11/14 3:38:45.000 PM kernel[0]: disk1s2: I/O error.
    6/11/14 3:39:08.000 PM kernel[0]: disk1s2: I/O error.
    6/11/14 3:39:10.000 PM kernel[0]: disk1s2: I/O error.
    6/11/14 3:39:23.000 PM kernel[0]: disk1s2: I/O error.
    6/11/14 3:39:46.000 PM kernel[0]: disk1s2: I/O error.
    6/11/14 3:39:48.000 PM kernel[0]: disk1s2: I/O error.
    6/11/14 3:40:01.000 PM kernel[0]: disk1s2: I/O error.
    6/11/14 3:40:23.000 PM kernel[0]: disk1s2: I/O error.
    6/11/14 3:40:26.000 PM kernel[0]: disk1s2: I/O error.
    6/11/14 3:40:38.000 PM kernel[0]: disk1s2: I/O error.
    6/11/14 3:41:01.000 PM kernel[0]: disk1s2: I/O error.
    6/11/14 3:41:04.000 PM kernel[0]: disk1s2: I/O error.
    6/11/14 3:41:16.000 PM kernel[0]: disk1s2: I/O error.
    6/11/14 3:41:39.000 PM kernel[0]: disk1s2: I/O error.
    6/11/14 3:41:41.000 PM kernel[0]: disk1s2: I/O error.
    6/11/14 3:41:54.000 PM kernel[0]: disk1s2: I/O error.
    6/11/14 3:42:17.000 PM kernel[0]: disk1s2: I/O error.
    6/11/14 3:42:19.000 PM kernel[0]: disk1s2: I/O error.
    6/11/14 3:42:32.000 PM kernel[0]: disk1s2: I/O error.
    6/11/14 3:42:54.000 PM kernel[0]: disk1s2: I/O error.
    6/11/14 3:42:57.000 PM kernel[0]: disk1s2: I/O error.
    6/11/14 3:43:09.000 PM kernel[0]: disk1s2: I/O error.
    6/11/14 3:43:32.000 PM kernel[0]: disk1s2: I/O error.
    6/11/14 3:43:34.000 PM kernel[0]: disk1s2: I/O error.
    6/11/14 3:43:47.000 PM kernel[0]: disk1s2: I/O error.
    6/11/14 3:44:10.000 PM kernel[0]: disk1s2: I/O error.
    6/11/14 3:44:12.000 PM kernel[0]: disk1s2: I/O error.
    6/11/14 3:44:25.000 PM kernel[0]: disk1s2: I/O error.
    6/11/14 3:44:48.000 PM kernel[0]: disk1s2: I/O error.
    6/11/14 3:44:50.000 PM kernel[0]: disk1s2: I/O error.
    6/11/14 3:45:03.000 PM kernel[0]: disk1s2: I/O error.
    6/11/14 3:45:25.000 PM kernel[0]: disk1s2: I/O error.
    6/11/14 3:45:28.000 PM kernel[0]: disk1s2: I/O error.
    6/11/14 3:45:40.000 PM kernel[0]: disk1s2: I/O error.
    6/11/14 3:45:55.000 PM kernel[0]: disk1s2: I/O error.
    6/11/14 3:46:07.000 PM kernel[0]: disk1s2: I/O error.
    6/11/14 3:46:20.000 PM kernel[0]: disk1s2: I/O error.
    6/11/14 3:46:32.000 PM kernel[0]: disk1s2: I/O error.
    6/11/14 3:46:45.000 PM kernel[0]: disk1s2: I/O error.
    6/11/14 3:46:58.000 PM kernel[0]: disk1s2: I/O error.
    6/11/14 3:47:10.000 PM kernel[0]: disk1s2: I/O error.
    6/11/14 3:47:23.000 PM kernel[0]: disk1s2: I/O error.
    6/11/14 3:47:35.000 PM kernel[0]: disk1s2: I/O error.
    6/11/14 3:47:48.000 PM kernel[0]: disk1s2: I/O error.
    6/11/14 3:48:00.000 PM kernel[0]: disk1s2: I/O error.
    6/11/14 3:48:13.000 PM kernel[0]: disk1s2: I/O error.
    6/11/14 3:48:26.000 PM kernel[0]: disk1s2: I/O error.
    6/11/14 3:48:38.000 PM kernel[0]: disk1s2: I/O error.
    6/11/14 3:48:51.000 PM kernel[0]: disk1s2: I/O error.
    6/11/14 3:49:03.000 PM kernel[0]: disk1s2: I/O error.
    6/11/14 3:49:16.000 PM kernel[0]: disk1s2: I/O error.
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    6/11/14 3:49:21.795 PM WindowServer[128]: device_generate_lock_screen_screenshot: authw 0x0(0), shield 0x7f8ef9e94e00(2001)
    6/11/14 3:49:29.000 PM kernel[0]: disk1s2: I/O error.
    6/11/14 3:50:48.000 PM kernel[0]: disk1s2: I/O error.
    6/11/14 3:50:48.546 PM com.apple.backupd[532]: Error: (-36) SrcErr:YES Copying /Volumes/Media/itunes Media/Mobile Applications/GarageBand 1.1.ipa to (null)
    6/11/14 3:51:01.000 PM kernel[0]: disk1s2: I/O error.
    6/11/14 3:51:13.000 PM kernel[0]: disk1s2: I/O error.
    6/11/14 3:51:26.000 PM kernel[0]: disk1s2: I/O error.
    6/11/14 3:51:38.000 PM kernel[0]: disk1s2: I/O error.
    6/11/14 3:51:51.000 PM kernel[0]: disk1s2: I/O error.
    6/11/14 3:52:03.000 PM kernel[0]: disk1s2: I/O error.
    6/11/14 3:52:16.000 PM kernel[0]: disk1s2: I/O error.
    6/11/14 3:52:29.000 PM kernel[0]: disk1s2: I/O error.
    6/11/14 3:52:41.000 PM kernel[0]: disk1s2: I/O error.
    6/11/14 3:52:55.000 PM kernel[0]: disk1s2: I/O error.
    6/11/14 3:53:07.000 PM kernel[0]: disk1s2: I/O error.
    6/11/14 3:53:07.747 PM com.apple.backupd[532]: Error: (-36) SrcErr:YES Copying /Volumes/Media/itunes Media/Mobile Applications/Glympse 2.22.444.ipa to (null)
    6/11/14 3:53:20.000 PM kernel[0]: disk1s2: I/O error.
    6/11/14 3:53:32.000 PM kernel[0]: disk1s2: I/O error.
    6/11/14 3:53:32.869 PM com.apple.backupd[532]: Stopping backup.
    6/11/14 3:53:32.869 PM com.apple.backupd[532]: Error: (-36) SrcErr:YES Copying /Volumes/Media/itunes Media/Mobile Applications/Golf Channel 3.7.2.ipa to (null)
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    6/11/14 3:53:33.376 PM com.apple.backupd[532]: Copy stage failed with error:11
    6/11/14 3:53:34.607 PM com.apple.backupd[532]: Backup failed with error 11: 11
    6/11/14 3:55:53.000 PM kernel[0]: disk1s2: I/O error.
    6/11/14 3:56:05.000 PM kernel[0]: disk1s2: I/O error.
    6/11/14 3:56:18.000 PM kernel[0]: disk1s2: I/O error.
    6/11/14 3:56:33.000 PM kernel[0]: disk1s2: I/O error.

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