just do not use discdoctor, it would probably make things much worse.
when i had no hdd in amiga, i used pc2amiga and undms.
but these days its adf this adf that. i'm sure there are free utils on aminet to do what you need, even though everyone likes that explorer thing.
parallel would be much much faster, but you'd need to be EXTRA CAREFUL with the cable.
oh,btw, if you got two floppy drives on PC, then it can read Amiga diskettes. but dunno if it could write them too.