It's most likely your MPU. Check my old thread about sound issues here;
https://pinside.com/pinball/forum/topic/explain-to-me-how-the-mpu-triggers-sound-on-a-wpc-sound-board
Not the same as your issue, but I began my troubleshooting just like you have done and found the exact same TANT capacitor burn on my board. Hopefully this leads you in the right direction.
A couple questions;
Leave the pin unplugged for a few hours. Plug it in. Is the sound normal?
When does the sound start to fluctuate? When the machine begins to get hot?
Does the sound fluctuate in attract mode?
I'm guessing the sound is fine at first. Then after playing for a bit everything goes wonky. This is most likely because an IC is failing and as it heats up it starts missing a beat and screwing up your sound.