How good is the rom dump? Does it work in emulators (like zsnes, I've never tried it in snes9x,) is it bigger than the good dump? You should use smc to check the checksum (not only tell if it's bad, but see what the rom says it is, and what it's actually calculated to.)
Most of the pins of the rom chip go directly to the s-dd1, so if you wanna dump the rom, I'm assuming your copier would have to know what to tell the s-dd1 to get the rom. I don't know if the swcdx2 can do this, but the best way to find out is to compare it to the good dump and see what's different between them.
I guess it wouldn't be soo bad to desolder 44 pins...