I've gotten a few scratched games over the years... BUG! refuses to load the last couple of stages, most notably, but Clockwork Knight 2's ending video skips and Mega Man X4 has some audio skips, too. I've recently wondered what I could do to effectively solve that; IIRC some enthusiast stores do resurfacing (or at least that thing where they grind away at the disc to remove the more superficial scratches).
There are some places around here that I can go to get discs resurfaced; I'll absolutely give it a shot if this second disc doesn't play. Worse case scenario, I bought a mint copy of PDZ and a coaster for $40.