I wish I had a working system 9 board that I could test, and expand my test ROM set with (http://pincoder.reversion.ca). Then I'd at least be able to give you some ROMs to try. I can't imagine system 9 is really that much different than 3,4,6, or even 7 - same CPU and PIA chips, etc - probably just higher capacity chips and located at different addresses. Still, I don't have anything to offer that you both probably havent already tried.
Is U41 still burning up? I only saw one reference to it in the schematics when I breifly looked at them, but perhaps Q6 and/or U32 need to be replaced.
U41-a (resized).png