Ok, so I tried cleaning it up more with some isopropol and qtip. It looks a bit cleaner, although still looks like it's covered in something the unit no longer passes the red jaguar logo.
Sometimes the logo is white and it just sits there, sometimes the logo bounces up and down, sometimes it's cut in half with the right side starting at the top of the screen and the left side starting at the bottom and they both fly up and away...
Sorry Saint, I didn't measure the IOL/IOR before cleaning it so I probably can't answer that question.
It did play Raiden and Iron Soldier properly before I cleaned it.
This is a unit I bought on ebay over a year ago which was supposed to work just fine. But I didn't try it right away, and when I did I got convinced by the seller that I could just get A/V cables (came with rf) and the sound would work. The unit came with the original power supply and neither of the chips I replaced looked like they had any problems. I only replaced them because I was starting to get excited by the upcoming flash cart and everything I was reading/watching online indicated that was probably the problem. After replacing them things didn't change.
I think this is going to be outside my abilities to fix based on the comments here.