Lion re-installed now my applications are asking for serial #'s and my old user profile won't show up during start up

What are all your applications that are asking this?

If you installed a fresh system via erase-and-install first, this is normal. You do not offer details. Otherwise, yes, after a clean install apps ask for re-introducing s.n.’s as long as keychain files are new.

Let me guess: you made a backup before installing the new OS (good thing), installed and, after making settings, you transfered data via Migration Assistant. Used AFTER making basic settings, it creates a new user, so your data are there, you should log out and relog into that user.

Used during the stup process, MigAssist does not create a new user. In any case, your data are there.

The weird thing is though that my old 'mark' user folder sis till there in Users..why can't I start up into that and run it like before?

I would echo that question back... why can't you log into that user? Does that user not show up on the list? Is there some kind of an error when you try logging in, and if so, what is it?

Also, we need some details on exactly how you reinstalled the OS. Did you just install right on top of the existing system, or did you erase the hard drive and then reinstall? If the former, I assume you were having a problem that prompted that... what was that problem? If the latter, did you use Migration Assistant or Setup Assistant to import data from a backup?