Usually a distorted input works fine PitchFactor. I haven't tried PitchFactor with a JCM2000 effects loop so I can't say whether it's the loop that is poor. Do you know whether it is a parallel or series loop? That makes a difference in the sound and you you should set things up.
Consider that if you did have a real guitar player playing harmonies, he/she would probably not plug into the same amp as you. They would probably have their own amp. If you are using PitchFactor strictly to simulate another guitar player
playing harmonies, then sending the PitchFactor's wet signal to another
amp would sound closest to the real thing.