That's a lot of questions all at once.
If your 15A MAIN fuse is good you should have~12VDC battery power (all measurements are to ground - the frame or engine metal) at the ignition switch, on the RED wire to the BAT terminal.
With the igntion switch ON you should get this battery voltage at the BLACK wire on the IG terminal. This black wire runs all over the bike, and the rest of your questions will need to be sorted out from further testing.
The lighting situation depends on where in the world your bike was originally sold (or, if the handlebar switch pods have been replaced, which market's version was used) as some places have headlight on/off switches and some have always-on headlights - the differences are considerable. However, you should have a bunch of black wires in the connection ratsnest under the tank behind the steering stem on the left side - this is where the switch pods connect to the main harness. These black wires should all have that +12V with ignition ON. The lighting switching is too messed up to try and describe, there are too many versions. Basically the power goes back and forth between the switch pods and the fuse box a few times before ending up at the actual lights.
The power for the spark coils is switched through the right pod by the kill switch, a black +12V power wire going in from the ignition switch and a black/white wire coming out to the coils.
The wires in the headlight shell are for the headlight and marker lights, the instrument illumination lamps and "idiot" light indicators, and the front brake and clutch switches.
The starter switch has a safety circuit that disables it if the bike is in gear and the clutch is engaged. Try the starter with the clutch lever pulled in: if it only works that way look for a problem with the neutral switch or safety blocking diode. If it never works, well... there are many possiblities.
