Arizona Warrior:
Maybe someone can check the circuits with those sensors the ECU only reads in 4th and 5th speeds?
The only
Input Device (sensor) that is gear related from the transmission is the
Neutral Switch 
.... if not in
Neutral the
ECU assumes the bike is in gear and in motion when a signal is received from the
Speed Sensor and so on
Just my .02 & opinion here: Trouble shooting a modern F.I. bike is much more challenging than an old carburated bike w/o a Black Box (Ignitor). A good analogy for automated industrial equipment would be comparing control relays and limit switches to PLC controls and prox sensors.
Often times the alarm/fault screen logic on a MMI (man machine interface) is more dificult to author than the actual program to automate the equipment.
The Warrior MMI is the Tachometer and our only way to communicate with the ECU software. The fault codes provided in the diagnostic mode can often times be misleading because the author hadn't covered unexpected failures such as: broken or poor branched common wires, etc.
Good example here is in the headlight. The ground buss could be a future problem with anything connected to it. Only 1-ground runs back in the main harness i suspect from this point. Other common wires for the engine sensors are branched with a mechanical crimp and taped w/o soldering.
Example: The rear fender harness is fabricated with branched mechanical connections and taped for the rear lights.
To trouble shoot some intermittent electrical problems might require unwrapping the main harness and validating a failed branch connection. THE ULTIMATE CHALLENGE!
Branch connections are common in automotive to limit harness diameters where as in industrial controls common I/O wires are generally run back to a main or remote I/O panel for trouble shooting for each device.

