This is a simple document on fuel injection
http://www.dpguzzi.com/efiman.pdfPage 13 shows the phase sensor that the air gap T must be 0.6 - 1.2mm tip to the target.
Of course you cannot get a set of feelers in to measure it, here's what I do.
1/ Align the target up with the centre of the hole.
2/ Put a small blob of quick setting epoxy or JBWeld on the tip of the probe.
3/ Bolt it in place with all its shims. (see Note after list)
4/ Allow time for the epoxy set up.
5/ Remove the probe.
6/ Peel the epoxy off the tip and measure it's thickness with my electronic caliper 0.6 -1.2mm if < 0.6 you need to add a shim.
7/ Bolt it back on and go for a test ride
Note: the epoxy won't stick to the target, normally it's oily, if not put a few drops of oil on it before step 3
BTW the efiman pdf is old but if you read it has a lot of useful information on how fuel injection works.
When you turn the key on the ECU closes the injection relay for a couple of seconds (strictly based on time), this runs the fuel pump to charge up the fuel manifold then the pump stops and waits for cranking.
As the bike cranks pulses from the phase sensor on the cam shaft tell the ECU it's cranking over and so it starts the pump starts again by closing the injection relays.
The ECU knows exactly where the engine is on it's cycle because there's a couple of teeth missing, it counts teeth from there firing the plugs and injectors at the appropriate angle.
I hope I haven't confused you.
Roy