Ever since I reconnected the neutral safety switch, the bike will not start in gear even with the clutch pulled in. I decided to test the clutch switch for continuity and sure enough it was dead. Popped it open to find the contacts all grimy and some of the copper corroded:
I cleaned everything up with some electrical parts cleaner, forgot to snap a picture after it was cleaned but I got all of the corrosion out and everything was nice and shiny. Slapped it back together and the switch is now working. Unfortunately the bike still will not start in gear.
Another problem I've been having is that the brake light does not illuminate with the front brake lever. I tested the stop switch in place and it did have continuity, but I decided to pull it off and check for corrosion anyway. The front stop switch has two phillips screws and a metal tab holding it shut:
The stop switch looked pretty good inside so I just cleaned it a little and popped it back on:
I guess the problem is coming from somewhere else. I traced the lines a little looking for a short or something disconnected but I didn't find it. I need to do some more tracing and testing wires it seems.
