Motorcycle Repair: Engine light off and on, throttle position sensor, efi systems

Question
Hello,
I have a 1999 HD Road King Classic that I recently purchased.  The previous owner had a 95" big bore kit, Andrews 203 cam, stage 1 air and stage 1 download on the stock ECM.  He also had a PCIII installed.  Shortly after buying it I realized it was running terribly, started hard, stalled alot and the battery was dying.  I replaced the battery but it didn't make much difference, still ran poorly so I brought it to a local mechanic, a good guy.

He had it a while then called saying that the older EFI systems (MM) were problematic and he wouldn't have recommended me purchasing a pre-Delphi bike (2001 or earlier).  He replaced both the camshaft and crankcase sensors, cleared the codes and removed the PCIII saying it wasn't working right on the bike.  He said its running well now however the engine light still comes on sometimes (about 50% of the time) then turns off again.  Since he had it over 3 weeks I wanted it back, he said if he had it longer he may have been able to track down the cause of the engine light but if he couldn't find it he may have to replace the whole harness.  He also gave the bike a full servicing (plugs, fluids, etc).

I just took my bike for the first ride since getting it home and checked if there were any codes and there was one, 42 (Camshaft Position Sensor).  The engine light was going on and off like it was previously but overall the bike ran fine.  Any ideas?
Thanks,
Kevin

Answer
Kevin,

The historic code data can stick for up to 50 ignition cycles.
Check the connections from the main circuit breaker to the ECM for loose crimps. Could be a loose ECM fuse or bad ECM relay to cause this condition.

Throttle position sensor might be out of range and
maybe need adjustment.

Lights flashing is part of living with these computer
systems. If it runs okay, it might recover on it's own
in time. Is the bike charging okay, battery up?

Sometimes the ECM's get moisture in them,
they can be removed and dried out with forced air.
Also, pulling the 5 and 15 amp ECM fuses overnight
might reset the module.

Best not to tinker too much with these systems
if it's running reasonably okay.