Not a bad idea to rule out the potentiometer, I've got a Xenon that sounds are cutting out on and it's for sure the potentimeter. Slightly different case, solder joints causing problems and not a "dead spot".. but similar idea. As soon as I put a little pressure on it, intermittent sound issues clear up.

I also had a Gottlieb System 1 machine where one of the speaker wires had not been soldered to the lug and was just resting on it. That had me chasing board problems, ROM problems, etc for a while trying to figure out why sound worked.. and then suddenly didn't.

Something else is to enter SOLENOID TEST via the self-test button, solenoids 20-29 during that test should be sounds. Could be a way to check if just certain sounds are affected.

The replacement cables are keyed at pin #29. Original cables could have been Molex parts with key pins, or ribbon cables that weren't keyed.

If you pop out the 6840 and bend pin #9 (IRQ) slightly outward so that when re-inserted it misses the socket, that will allow you to disconnect IRQ and you can then just remove the 6840 again and bend it back straight after testing that theory. Just bend it very slightly -- you don't want to put a kink in it or it'll snap off... just needs to "miss" the socket when you re-insert the chip.

If you need help finding pin #9.. with the chip oriented so the notch on the top of the IC is on the left.. pin #1 is the left-most pin. Count over to pin #9 starting at that pin.

Apparently if you wreck than IRQ pin, it doesn't matter since it's being said IRQ is not used at all

Other option is if you have the old set of cables, try those.

If you only have the new cable, your only other option would be to use a very tiny flat-blade screwdriver (from an eye glass set for instance). You can release the Molex pin on one side of the cable by pressing in the locking tab on the pin (there's this slot/window on the back-side of the Molex connector where you should be able to see the locking tab). You'd need to push that in so it no longer catches inside the connector (locking the pin in the connector). Only thing is, they're kind of a PITA to bend back if you're not used to doing it.. since you have to push the tab back the opposite way so it can lock again.

I'd just lightly bend pin #9 out on the 6840. You'll be okay that way and it should be pretty quick.

Is that with the Alltek in the game or back to the original board?

Also is there a setting on the Alltek for "MPU-200" ?

Yeah, clear the audit data as was suggested. If that doesn't do anything, just for the heck of it try leaving the J1 harness disconnected from the MPU & play a game "blind" (ie. no displays, no feature lamps). Start a game and trigger switches for sounds & see if it sounds the same. You may also want to try going into Solenoid Test again.. only with the playfield switch harness (J2 on the MPU) disconnected.