Figured I would mention my findings with HP Tuners and the switch I put in. Just putting the switch in seems to have fixed the problem, which doesn't make a whole lot of sense to me. I put the switch on the data wire going into the module. It originally had two data wires connected to the same pin. I soldered those two together, ran them into a switch and back into the module. My first try with the switch off gave me problems, couldn't read the pcm. Then it wouldn't read with the switch on either. I reset everything and left the switch on, now I can write in high speed even with the module on and it quit making noise like it used to. So all appears to be good for now.
COTY - 2012
Tom - 03' Bonneville SSEi', 00' Sierra SLE, 1980 Goldwing GL1100 Interstate