I haven't worked on the sound in a Punch Out for a while, but I just fixed the sound in a DK3 today.
Pull out the schematics. Find where the speaker hooks up. Work backwards from there and see where the schematics head to. Nintendo likes to have 1 section make digital sounds (like music) and 1 section make sampled sounds. My board had some of the samples missing... so I poked around with a logic probe, and the 2115 ram chip had several lines that were stuck 'hi' instead of pulsing. I looked at another 2115 ram chip on the board, and it was pulsing on most of the lines. Swapped the 2115 ram out, and it fixed the sound problem.
On the DK3, it had two crystals, one to run the program, and the other to run the sounds (at a different frequency) so Kbojjn may be right about that.
Since it's playing it, but it's just messed up, i'd say it's some sort of TTL chip, not a rom or something.