Trying to get back into the swing of things post-Time Machine

Question

So I recently had to wipe my MacBook Pro clean and reinstall everything (*****!)....
I'd done a back-up on Time Machine, and went to restore the files from the previously backed up session. Now, for some reason, Time Machine told me that there wasn't enough space on my laptop's hard drive to restore that session. So using the program Sync Two Folders, I was able to basically replicate everything that was in the back-up but not on the laptop (confusing yet?).
Only problem is, there are certain holes still:
1) I don't have anything in the cache of Firefox, meaning that all my bookmarks, passwords, etc. are gone. Isn't this supposed to be recovered in the case of a restore?
2) Certain applications I have seemingly need to be totally reinstalled and registered (Reason, Pro Tools). Is that normal, too?
Am I missing something here, or is this just part of the pain of having to erase and reinstall a hard drive, even if you DO have it all backed up?

Answer 1

What you missed is that applications are not just in Applications. There are application support files, preference files, hidden registration files, Unix files, etc. Syncing two folders only gets a part of the job done, hence why you use a backup - to restore the backup. But you can't restore the entire backup because you've already installed OS X which takes up a good part of the backup.
What should have been done was after installing OS X and going through the Setup Assistant you were offered an opportunity to restore your files from a TM backup. You should have taken that option.
Or you could have reinstalled OS X to find that the installer would have provided the option to restore the system from a TM backup..
Note that reinstalling OS X means you would have erased the hard drive first.
You may be able to get things back to near normal by doing things manually. See the following for information on what needs to be transferred:
Folders You Can Move to Your new Mac
From the Home folder copy the contents of Documents, Movies, Music, Pictures, and Sites.
In your /Home/Library/ folder:
/Home/Library/Application Support/AddressBook (copy the whole folder)
/Home/Library/Application Support/iCal (copy the whole folder)
Also in /Home/Library/Application Support (copy whatever else you need including folders for any third-party applications)
/Home/Library/Keychains (copy the whole folder)
/Home/Library/Mail (copy the whole folder)
/Home/Library/Preferences/ (copy the whole folder)
/Home /Library/iTunes (copy the whole folder)
/Home /Library/Safari (copy the whole folder)
/Home /Library/Calendars (copy the whole folder)
If you want cookies:
/Home/Library/Cookies/Cookies.plist
/Home/Library/Application Support/WebFoundation/HTTPCookies.plist
For Entourage users:
Entourage is in /Home/Documents/Microsoft User Data
Also in /Home/Library/Preferences/Microsoft
For FireFox:
/Home/Library/Applications Support/FireFox
/Home/Library/Preferences/org.mozilla.firefox.plist
Credit goes Macjack for this information.