I feel very sorry for you.
MCR boardset are one of the biggest pains to work on. First of all, the way they're put together doesn't lend well to debugging them, and the web of harnesses that are hooked up to these boards doesn't make it any easier.
My advice would be to replace the ribbon cable connectors with known good ones first before you go any further. Second, make sure all the dip switches are set correctly, as there is a dipswitch mode which will cause the game to look like it's not working. Then I'd check out the following documents below.
Clay Cowgill made up a debug EPROM for the MCR sound board. It allows you to trigger certain voices and functions on the sound board via the DIP switches. You can then trace the sounds through the board and find bad opamps, etc. Burn the EPROM and follow the instruction text provided.Download Debug EPROM zip file