Well, lets look at all the facts.
1) Bike cranks. - Not a battery issue.
2) No dash lights - a wiring issue.
3) Indicator lights staying on/lit - a wiring issue
Blah, blah, blah - All comes down to a wiring issue. I SUGGEST you take the fairings off and start tracing the wires from the HID's back into the wiring harness and checking to see that the wires are Soldered into the main loom and well insulated/taped up. From what you describe, something has rubbed, caught, worn and is causing an error to the ECU. Remember that the wires that go to the dash also go to all other sorts of things, like indicators, kill switches, clutch switches brake lights, head lights and so forth.
For the power commander, make sure it is grounded properly and that ALL the plugs are connected solidly to the fuel rails and the TPS (Throttle Position Sensor) which is a real little PITA to get to.
Good luck and I will be interested to see how you go.