1988 Mustang 5.0 lx, ignition problem

Still having problems with my 5.0...changed ignition module, spark plugs, wires, cap and rotor and coil, and cleaned all connectors, bur still the engine refuses to make it over 3500rpm's under load,,,with no load, and a light pedal it makes close to 6000 rpm's...can it be an incorrect ignition module?? got it from ebay.... Is it true there is a difference between manual ant auto trans mission modules??