If the headlight is going out when you hit the start button then your battery is too dead to run the starter, pump and headlight at the same time. Put it on a charger overnight and try it the next day, make sure you trickle charge it, not generally a good idea to recharge a dead battery overnight at 10 or more amps.

 

As for the original question. Check the connections on the two relays that are attached to the right side of the undertail compartment underneath the rear tail fairing. One of them is your Fuel Cut Relay the other is the Engine Stop Relay. You might have unplugged one of the plugs or wires going to those relays when you pulled your tail fairing off. If your fuses are fine and it started fine before you took the fairings off that would be what I'd check next.