Please explain, how did you jump the gear position switch? Cause if you make a mistake there...? Well, lets not get into that just yet. Have you downloaded and read the service manual yet?
My advice is to start with fixing your known issue correctly first. Fix that gear position switch. Undo any cobbles, splices or jumpers that you've done. Keep an eye out for a pinched or fried wire while doing that work. Ya gotta read and follow the service manual to work on that bike, so make that a priority. There are no shortcuts free of consequences.
We can't see or review whats happened, so most of this diagnosis is in your hands.
I'll try to follow along once per day if I can. Right now the site is logging me out constantly, so if you don't hear from me its because I've given up. Perhaps others can help ya better anyway...