Wow- that took a while. But- last install went through fine. A couple of things to note:
1. exp_captchas was huge- and honestly can be truncated no problem. It was throwing memory errors trying to deal with it- thus the 400 errors. Basically? I just emptied it via phpmyadmin before running the update. That got past most of it (and I’ll add truncating the table to the updater- I did it already, but I still had to empty yours manually first. So if it comes up for anyone- truncate exp_captchas if it’s hugge (was 55mb almost 800,000 records).
2. Make sure the database doesn’t have any tables it shouldn’t. The backup had some from 2.0 in it- snippets and such. Threw an error on me- but once I noticed they were there, I just dropped those extra tables when I truncated captchas.
3. Had some duplicate records in exp_category_posts- which will throw an error when EE tries to add a combined index. I’d already put a check into the next version of the updater, but hadn’t tested it out. It needs a few tweaks, but was sufficient for handling this case.
4. I upped the memory to 256- which is probably not necessary w/the captcha table reduced. But I did that first- and it wouldn’t hurt to leave it that way when you run the update.
Oh- and because I didn’t want to remove/rename the install stuff- in index.php I ‘fidged’ the check that makes you remove the folder:
// Is the installation folder present?
if (FALSE && is_dir($system_path.'installer/'))
{
The FALSE bit shouldn’t be there- but for testing it’s a quick way to have it skip that check.
You’ll want to use the contents of the current install folder if you go in to do this yourself. I put some new files up. If all is well ‘as is’- you can go ahead and delete the install folder and proceed as normal. I can tell by looking at the cp login, some paths and such will need changing. But the update itself went through fine. After a good bit of tweaking 
Thanks for your patience and allowing me to experiment with your install.
If you have any questions about what I did- just let me know.