I think it's important to work on one problem at a time. I would ignore the sound and the DMD for the moment and work on your switches.

It looks as though you've installed a known good CPU board, so I would start with the switch problems and the switch matrix, which is part of your driver board. I have a System 3 manual, but not for this game. Take a look at your switch matrix and see if the problem switches all share either a strobe or a return. If they do, are there any switches on that strobe/return that work properly all of the time?

I think that the "Playboard" is sometimes referred to as A9. When I compare this to the switch matrix for Stargate, all the pins and strobes line up on the connector for A3J3, which is the driver board so I think that's where it goes eventually.

On the bottom of the playfield, your strobe line basically daisy chains from one switch to the next. Because your problem is intermittent, I would suggest checking all of the solder joints along that line. Wiggle each wire a little as though you want it to come loose. If it's a proper solder job it won't, but don't yank just wiggle. The strobes originate at the CPU. Because you've already changed that out, I see this as a likely wiring problem.

As viperrwk already mentioned, the strobe 1 line is also driving a series of lamps. Check your lamp matrix and make a note of which ones. Do a test and ensure that they're working properly. When you notice that your switches aren't working, check to see if the lamps stop working too. If the problem is shared between lamps and switches, we can focus on the parts of the system which they share.

Oops. It looks like I read the schematic wrong. The timing for the strobe comes from the CPU, but the individual strobes are from the Driver Board.