Problems after TM restore

After replacing a dead hard drive, I was able to restore from TM. However, I've been having problems ever since and I'm wondering if it is a problem with permissions.
I can't drag/drop folders or files anymore in the Finder. I also can't use iSync anymore... get a message that the sync server is taking too long to start.
Any ideas of what could be going on here? I tried repairing permissions and also tried deleting the Finder.plist file.
If I do a complete reinstall of OS X, is there any way to only pull back the folders I want, and not overwrite the system files/permissions?
Thanks in advance,
John H.

From the OSX install disk you can choose to install a new system folder without deleting the old one, just renaming it. Then you'll have to move the system files you want to the new folder.

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