Upgrading to Mt.Lion - How do I ensure no problems with ownership of files while only copying some documents over?

I have a macbook pro 2011 and I'm planning to upgrade to Mountain Lion when it is released. I currently have time machine backed up on an external hard disk. However I do not want to do a full restore after upgrading to Mountain Lion, but i do want to extract certain files from the time machine backup. Is this possible?
The last time I tried copying files from a time machine backup from another mac to this mac, I had permission issues with files. How do I prevent these issues? I read online about something called setup assistant but does this just copy over user accounts? Does it copy the home folders too?
Thanks for the help

The setup assistant copies the entire user folder. You can't pick and choose.
A "Clean" install is generally a complete waste of time. Depending on what you want to leave behind, it might be simpler to just remove that stuff after the fact. No issue with permissions that way.
But, if you really feel like doing that, you'd have to do the Browse Other Backup Disks thing with Time Machine and restore what you want. Just restore to the Shared folder, then move to your home folder. That should mark them as owned by you, and not the old user. I've only done single files, so I don't know what might happen with folders full of stuff, like the iPhoto Library.
Having erased the drive, you'll have to reinstall all of your software. The iLife apps come with a Mac, so they won't get installed with Mountain Lion. You'll have to reinstall those from the App Store or Disk if that is the case.
I don't know what happens when you try to restore your bundled iLife apps, but this article indicates it is possible: http://support.apple.com/kb/HT4718

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