Alright, I decided working with the source project was just too much.
I got a fresh install of dotnetnuke, I brought the module code to 2.0 code recompiled and made the one version change needed (DataCache.ClearTabCache to DataCache.ClearTabsCache). put the dlls into the bin folder, copied my Code folder into DesktopModules. Made the sql connection and machine key adjustments to the web.config, then brought up the page and let it do its Upgrade.
I got one error
00:00:04.468 - Executing Script: 04.04.00.SqlDataProvider Error! (see 04.04.00.log for more information)
I wasn't ever able to find that log file, so no idea what happened there.
Then when I tried to map to my Default.aspx page, I got a Redirect Loop.
I tried every single fix I could find on this. My Alias was fine, I tried removing the Web.Extension.dll from bin and upgrading the assembly reference to 3.5.0.0, and even tried the old version of the Default.aspx page, nothing worked.
I get to the same dead end when I try an upgrade with the already existing Folder (instead of using a fresh install) and copying over the existing folder with the new install files.
Is there any way to fix this?