2000 FLHRCI, 35k miles. On occasion, when I put the run switch in run, the fuel pump doesn't run nor do I have spark to the plugs. Eventually, with some digging around fuses, relays, connectors, etc. the problem will go away. Bike has a Power Commander III USB on it now for 20k miles and everything was fine until about a month ago. Once the bike starts, no issues.
My Indie checked fuel pump, run/stop switch, coil, tilt sensor, map sensor and crank position sensor. All good. I thought maybe bad ECM but after reading forums that seems to be quite rare.
Any ideas

 

Loose pin connectors that the fuses go into.

 

Disconnect power commander. See what happens. Verify crank sensor.