The interlocks for crank and 'run' are different:
For starter, only interlock is the clutch switch
In order for engine to run, it needs to see Neutral OR Side-stand-up - I just suggest to raise the side-stand as it simply eliminates the neutral switch as a possible factor
However ..... the Coils and the Fuel Pump get their +!2V from the same source, what is actually designated as the Fuel Pump Relay (but it does actually also supply the ignition coils) - this relay is what would be shut off by ECU in event of the neutral/side-stand interlock being made: so fact that you have pump run & ignition pulses suggest that the interlock is satisfied.
The injectors get their +12V from the main power relay - that also enables the ECU so you would have to believe that should
also be good - but you should validate that you do indeed have 12V on the Brown/Pink wires on each of the injector plugs with respect to battery negative (there should also be an unused junior timer connector in that same harness that has a brown/pink and yellow/red wire - you can also just check for the 12V there on the brown/pink - but again with respect to battery negative NOT to the Yellow/Red); all of those should be 12V with ignition on.
If you confirm the 12V is there, next check to see if the injectors are actually firing - put a screw-driver against the solenoid and crank the engine (helper would be useful) with your ear on the handle - you should hear it clicking. If it DOES click then you don't have enough fuel pressure if it is not spraying fuel - that then puts you back into the pump. You said it sprays fuel - are you confident that you have 45psi there? It's easiest to check as I described - simply unplug the return hose quick connect fitting - the top one. (the original male hose fitting would have been a plastic one with a valve - the valve would have to be depressed to open - however this should have been replaced under recall with a metal one and those have no valve) To properly check the fuel pressure, the fuel circuit needs to be complete as the regulator is after the return fitting - a pressure gauge then needs to be tee'd off either of the hoses.
One other check - I can't tell whether your model has a ground block or not - they changed the grounding scheme somewhere along that first model year, my understanding is the very earliest do not have the ground block which is a common failure point. This is a common grounding buss where all the systems' grounds come together - it is located just in front of the battery box, sometimes is encased in foam. The block gets burned and some circuits lose their ground - this can even affect the ECU. So look to see if you have one, if so remove the cap and inspect for burning