Okay I finally figured it out after reading about a hundred pages of threads... ugh...
There are many options in the registry under HKLM\Comms...
If you set the AutoRunFlag to 1, it will BYPASS the autorun on every hard reset.
If you set the flag to 0 (or i imagine if you remove the key entirely) it will run the autorun in the windows folder.
It seems that it also ignores the registry keys that tell it to go to EXTROM, since newer phones don't have EXTrom... So for my purposes I just dropped the rom I needed into the "Additional Sounds" cab, modified the RGU to turn off the autorunflag, and had it run everything from the windows folder, ignoring the now useless extrom.
Hopefully someone else will find this useful someday, save them the hours of searching
