Constantly need to repair disk using Recovery HD to get Lion 10.7.2 to boot

Question

I have a Macbook Pro 17" 2.8ghz I7 with 8gb of ram, OS X Lion 10.7.2, model series MacbookPro6,1....
Every time i reboot the computer or turn it on i get past the gray screen with the apple, it begins to load my desktop but stops just before it finishes loading everything.  I can see my background image, some of my desktop icons, anywhere from 1/4 - 1/2 of my icons at the top, then i get the pinwheel and it doesnt progress any further than that. 
The only way that i can get the computer to boot after this is to hold down the power button, wait for it to turn off... wait 20 seconds, reboot into the Recovery HD and use the disk utility to repair disk and repair permissions on Macintosh HD. This usually works, but one time i actually had to download a new copy of lion.  After i repair disk & permissions, i reboot the computer and it responds like nothing has happened.  My problem is that i do not want to have to constantly repair the disk and permissions every time i reboot the computer. 
I did have one problem before all of this began, but it was about a month before this started occuring.  I sent a bunch of unneeded documents and duplicate files to the trash as well as a couple of programs that didnt work anymore using appcleaner.  When i tried to empty the trash, it deleted all but one file, or should i say most of the file.  It was Dragon Dictate... it deleted everything from the main app package except for a plugin file.  The plugin apparantly took up 0 bytes on the disk, and nothing i could do would allow me to delete the file.  Finder froze every time i tried to delete the file, or should i say hung at the emptying trash window.  Finder was still working.  I could still open windows and move files around, however, i couldnt get the trash to empty.  I left the screen up all night into the next afternoon, and it still hadnt deleted the file.  The only way i could get it to not hang was to remove the file from the trash, and delete what else i had to delete.  The only way i was able to get trash to stop hanging was to force relaunch finder by going to Finder>>Force Quit...>> select finder>> relaunch.  Sometimes finder would relaunch, and sometimes it wouldnt. The only guarantee that i had to relauch finder was to reboot the computer.  Eventually i jsut moved the file to a folder named Can not delete..... Now a month later i have to repair the drive each tiem i want to reboot the computer.
I know the drive isnt failing because i dual boot to windows, and that works flawlessly.  No problems with reading/writing, other permissions, hardware, software, bluetooth, network, monitor, sound, camera.... nothing wrong on the windows side. 

Answer 1

Your problems started when you used AppDelete, it searches for files and can accidentally delete some files as well.
You should never use such a program, it's no subsitute for the developers uninstaller.
Because your issues reside in the Applications folder, a global use, your going to have to perform a backup, erase and resintall of Lion, all your programs and return of files from backup.
As you learned, a OS X overwrtie install isn't going to work.
Also when you use Disk Utility to Erase the Lion Parititon, use the Erase>Security Opiton> Zero aspect, it takes longer but maps off failing sectors which may be responsible for your issues and ones in the future.
Map off as many as these failing sectors as possible, with Zero Erase and Erase Free Space once in awhile. SSD owners need not apply.