Applications :: Time Machine Reinstall - Applications Crashing On Mac

I recently reinstalled OSX 10.5.8 on my penryn MBP so I could make a larger XP bootcamp partition. After reinstalling leopard and restoring my whole system through time machine my computer is acting weird. First, "the file "itunes library" cannot be read because it was created by a newer version of itunes". It didn't upgrade itunes to 9 till after I had done all the TM restoring. should be older, no? Second, adobe applications crashed. I was in AI working on a 500 mb file and BOOM, beach ball>crash. All other CS3 unable to open. I have 4 gigs of ram and some of the applications that would not open were not even in use at the time of the AI crash, could this be something with the TM backup? CS3 was all installed together.

Third. While this epic crash is happening on my desktop disappears. Just a blank desktop image. but wait, If I click were things used to be, Bam they appear out of no where, but only if I click where it is supposed to be. It's there in the desktop folder but not showing up as icons on my desktop. I think this has happened to me before the reinstall too, though never all at once, usually when I use the "pinchy" to resize icons one or two will disappear. Fourth. Cisco clean access agent beach balls and requires hard reset. the login window was floating on screen all the way till the screen turned off. These all happened in the same day, now It is working some what like normal, though my itunes is broke. Any ideas on how to fix this itunes? If I only need one application and it's plug-ins (SU and Podium beta) restored through TM ( i have a disk for all the others) is there a way to just restore the one. Would this give me a more stable system over all? should I go ahead and reinstall and restore the one app and do the rest manually?