Okay, I'll give you a few things to check.
1. When you turn the key to the on position, do you head the fuel pump priming? It should hum for around 5 seconds, this is a different sound then the subthrottle valve clicking and beeping. If it doesn't prime, then there's a good chance your vehicle down sensor is triggering and broken. The FI light should be on if this is bad though, so if the pump doesn't prime and the light is off, then your gauge is bad, or the ECU is bad.
2. Pull off the plug for the radiator fan switch, use some insulated wire and connect the two leads inside the plug. Your radiator fan should come on, if it doesn't, your sub-harness either isn't connected or is bad.
3. Make sure you have the correct plugs, if you do, check the primary and secondary windings on the coils, checking 1 or 2 is sufficient, there's practically no chance they're all bad, but you never know, these bikes aren't getting any younger.
That's the quick stuff to check, if everyone is within spec there, lets move on to the interlock system:
Get your multimeter out (should already be out for windings) and head to the junction box. Set it to 25V DC and connect the (+) lead to the G/BK lead in the junction box and the (-) lead to your frame ground. With the transmission in first, the clutch lever released, and the sidestand down, turn the ignition to on, and you should get 4volts or more. If it's under 4 volts, check the sidestand switch, starter lookout switch, and junction box. If they're fine, get a new ECU. If the voltage is 4volts or more, hit the starter button, if the starter turns, the ECU is bad. If it doesn't turn, then its fine, and proceed to check the rest of the starter system circuit.
Before doing all that noise, are you even getting power to the coils? Stick your multimeter on the wires up to the coils. If you don't have the proper adapters then just cut into the wire on one of them and leave the coil installed but no plug. The red is your positive wire, and the black is the negative, put the multimeter at x250V DC range and crank the engine, you should be getting 100volts or more. If you aren't check the crankshaft sensor.
So, for the crankshaft sensor...back to our friend the multimeter. For the first resistance measurement check it at the sensors lead connector, the connectors are near the rear brake fluid reservoir. Measure the resistance, it should be at 460-470 ohms. If it's higher then the coil has an open lead and replace it, if it's less then there is a short in the coil, and replace it. And on the connector, it's the two leads on the bottom and right, if you look at it with the clip on top. Now change your meter to the highest setting, individually connect each lead to the frame ground, if it's anything but infinity, it's shorted, replace it.
If that's fine, then check the voltage. Turn the meter to the 10volt DC range, connect the negative from the adaptor to the bottom middle of the connector, it should be black/yellow. Then connect the positive of the adaptor to the bottom right, it should be solid black. Then pull in your clutch and hit the starter for about 5 seconds with the transmission in neutral, it should be 2.0volts or more. If it's not, take a guess at what to do, crank sensor first, then the ECU.
If those are fine, you could be super thorough and check the continuity of the wire. The black wire out of the sensor ends up at the 24th node/terminal/plug/etc. of the ECU, and the yellow/black wire ends up at terminal 11.
I'm tired of typing, do all this and reply here and I'll find think of some more crap to diagnose.