Hopefully a Kentico support person will chime in, but if something botched, there are some options to consider (but do these on COPIES of course)
1: Try installing a fresh install of Kentico 10, then copy your custom files and code over to that, and change the database to point to your instance. Kentico is just files and database, if the database updated properly but the files didn't, sometimes just starting from a fresh kentico install file set and copying custom files is easiest.
2: You can do #1 but instead of copying custom from yours into the fresh, look to copy the LIB/bin/global.asax / .csproj files over from the fresh to your copy, perhaps those just didn't upgrade properly? Also do a text compare to see any differences between your web.config/cmsapp.csproj and a fresh, maybe you'll spot an error?
3: You can try re-doing the install processes, and don't change the code files until after the upgrade, i doubt it but maybe the early change messed up something that is required during the install...but again i doubt it.