How to selectively copy parts of my Time Machine backup onto my new OS (Yosemite)?
Typically the migration assistant doesn't copy system files from your backup.  But you're right that maybe one of your home-folder's installed files (a PrefPane or something) could have caused your problem.

I would still run the full Migration Assistant (just let it run for however long it takes), and hope that the problem doesn't come back.  This is typically the case.

If you problem does come back, then you know it stems from your home folder, in which case you can boot while holding Shift down, to disable all non-essential extensions/plugins.  Then you can remove all 3rd party files from /Users/HOME/Library/PreferencePanes, LaunchAgents, LaunchDaemons, QuickLook, Services or whatever type of error you think was happening.