I'm gonna go out on a limb here. I have no idea what priority you have on this project, or how much revenue is at stake. I can see you have had a lot of trouble and frustration. People on this forum will absolutely help, but replies back and forth will be slow, and lacking access, we won't always see the gotcha issue.
There are people who deal with these upgrades for a fee, and lat9 who has been helping you is the one ofthem i would first recomend if she has time for another client right now. If not, there are several others. Not saying you can't do it, but if your tired of it, there are options.
My personal guess is that your old db has various corruption that will need fixed before upgrading. Might try the audit plugin on the old site as it can find some of it.