Headlights and signals unhooked shouldn't affect anything.
Have you bypassed your PC and tried to start?
The connectors are just under the left rear of the fuel tank, tucked on the inside of the frame.
The other switches you mentioned about checking are bank angle switch and sensor, neutral switch, sidestand switch, and clutch switch.
I believe if your fuel pump is working, and you're getting fire at the plugs, and it runs on ether, then all of the above switches are working properly. imo.
From what you described, (which is cool that you list all the things you've already done), it sounds like the injectors just aren't getting the signal to hit.
I don't really know that area well enough to advise, but your switches are probably ok.