Yeah, I'm not sure about jiggling harnesses while the game is on- However last night I spent a couple hours replacing all 4 connections on the MPU.
Interesting, this board (It's a stern MPU200) has a header that isn't being used. It's a big one too! And, there is a large IC next to it, I think it might be the 6800 chip. Anyway, there are two pins. It looks like #1, and maybe #12 or so. for some reason they have created secondary connections for these two pins. They soldered wires directly onto the chip leg, and around to the underside of the board - I gather because the socket was bad. I've left well enough alone with that situation since I don't have a replacement 6800 chip at the moment.
Good news though, after replacing the 4 headers, I was able to get the game to come back up! Seems like I always have problems with the initial installation- I change the headers, and reflow any obvious cracks, and sometimes, if say a an added jumper wire is OBVIOUSLY too long and is causing hinderance when installed, I'll fix that.. And I saw a place where it looked as if they had globbed a bunch of solder on, so I cleaned that up a little. However it turns out that little glob was supposed to be there because it was fixing a trace that was somehow not working. They had fixed it by flowing a little extra solder on top of the almost non-existent trace.
Anyway, I plugged it all back together and she still runs at least! Also, during my first test game - It was 2am by this point - the game was consistent, and the sounds didn't get all screwed up. I haven't seen the displays crap out since I replaced them, but I hadn't been playing for very long.
-Brian