Ok, I wasn't going to post about this but as it's turned out to be quite a complex fix to track down then maybe this will help somebody.
For a long time, even before starting the restoration, the game has had a problem where after being turned on for a few minutes if the left ramp switch is activated it causes the audio to completely break up with some nasty pops and clicks. The DMD also starts to flicker. Here's a short video showing what I mean:
I'd spent a LONG time trying to track down what was causing this, everything from switch diodes to reburning roms to completely rebuilding the sound board. Turns out the problem is caused by the new XPin Power Board. The +12v circuit is not strong enough to supply voltage when the rope lights are switched on and flashing. Voltage drops to around +9v and causes the amplifiers on the sound board to give up.
Good news is the board is easily modified to fix the problem. XPin have a 2 year warranty on their boards but there is no need for replacement. This is a fix for the Revision E boards. The problem may have already been fixed for later versions.
2 simple changes should be made. First of all, the regulator VR3 has its legs snipped and the pads on the board joined together. Second, the capacitor at C1 is massively underrated at 10,000uF. The original Data East power supply uses an 18,000uF cap. So, I've changed that as well. The result:
The game now works flawlessly, and has a good strong voltage on the +12v circuit, dropping only to +11v when flashing the rope lights.