Love your progress on whack a mole.
Just curious are you planning on reusing the original MPu and boards from machine or are you going proc and mpf route.
Secondly I notice you added the chimes into the machine. This may distract from your point sounds and mp3/wav sounds.
My assumptions with the retheme is you will want the proc and mpf solution.
This will completely take care of your sound effect direction.
If that is not the case I can make a few suggestions. In my case I did the Arduino mega and the raspberry pi route.
For me the Arduino was the brains and trigger sensing events. It transferred all game event triggers to pi and it played them back. The pi was also the back glass driver but everything was messaged to it real time by Arduino.
Let me know what your thoughts are. You can check out my Arduino conversion of Close Encounters thread to see what I did.