i just removed the factory unit in my 88 N/A. The speaker wires still go through the external factory amp below the glovebox. Question is should I leave it like it is or is the amp in series making it worse since it has a lower output than the receiver???

I would just try running another set of wires to one speaker from the new head unit, you dont even have to actually route them where they belong, see how it sounds, and make your decision from there, you can compare it to the other speaker running thru the factory amp.