The EPROM should be fine, they're bullet proof. What are you running the synth output into? A guitar amp, mixer etc? The volume level out of the synth/guitar mix socket will be roughly the same as a guitar output level - a fair bit quieter than a normal line level synth.
Have you replaced ALL the capacitors on ALL of the boards (including the big main synth board, not just the rectangle string trigger boards)? Synth sound related issues will relate to the main synth board, if all things are equal and all strings are triggering properly. There is a capacitor on the synth board that I had to replace.
Make sure you replace all of the caps on both trigger boards - people often stop at the uppermost board because it resolved their problem but the second board also affects triggering levels and can contribute to a pseudo distorted sound. Do the lot. I did and it fixed all of the sound and triggering level problems.
Cheers, Graham