Yes, after uploading new files and overwriting the existing ones i did run the php script to start the upgrade. There was one warning do to with "counting" and the rest was successful.
database errors surely wont be inheritent problems as these missing fields and tables do exist on my database backup.
if u were to make a fresh install, i would only be backing up the database with these things missing again..
might be an idea to make a fresh install somewhere else and compare and tweak see more things i guess