Transferring individual files and applications from time machine

Hi there, a few months ago I was having real problems with applications refusing to open and some things freezing. The guy in apple store reformatted the hard drive and then recovered everything from time machine. Helped a little for a short while but was never great. In this last week the same things have been getting completely unbearable so I thought I'd try installing maverick, in case that would help. Downloaded the installer, but like a few of my other applications it just refused to open - sitting in the dock with a white dot, doing nothing.

So I decided to format the hard drive again and start again, thinking I could transfer files and applications from my external drive (holding time machine backups) and hopefully that transfer wouldn't take with it whatever clashes or corruptions are causing all the problems. I formatted it and installed mavericks and that was fine; but when I tried to use migration assistant (as some website suggested I should) I found I could only transfer all the applications, for example, rather than selecting them one at a time. So I selected applications and it started transferring but then completely froze up. I eventually tried turning the thing off and on but it wouldn't boot up. So now I've formatted it again and am installing mavericks again, but once I have I'm not sure what to do. Any ideas? I need virtually all the files and applications but I really don't want to end up with the same issues again.

Cheers

Btw- please assume I know absolutely nothing about this kind of thing, if it wasn't already obvious!