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Hi and welcome to JustAnswer,Thank you for the question and your patience. Should you still need assistance for information purposes only...Initially, proposed preliminary tries (if have not been done):
All other checks would be with the use of a multi-meter particularly on the electronic components of the relay assembly and the presence/consistency of the IGN+12V.
Still, attempt to start again with throttle partially open. Other checks (also if have not been done) to consider/try:
With a good/fully charged battery, the Yamaha should be able to start and run even with the rectifier/regulator disconnected.
On "...spark plugs were cleaned today and put back in..." please confirm, spark at the tip was visually checked. ...and did the plugs got wet with fuel?
That fuel pump has power would indicate that there is IGN+12V to the ignitor and the red/white wire to the relay assembly.
Consider a hardwire test. Temporarily connect a wire to engine/frame ground from:
Please post back results / observations of the above once tried.
Attempt to start on all instances, observe starter motor action and for presence of spark.