I’m at the same place you are, with the same PHP files involved. I tried uninstalling all of my plug-ins to no avail. I suspect the database too, but I was using WP 2.5 and am bringing in a database from that set up.
I’m going to try what you did and delete the tables and see what happens. I’m fearing a compatibility issue too and having to rebuild my blog. Add me to the list of any advice would be appreciated at this point.