bikes looks so cool i hope you get if figured out. I have / had a KLR today i decided its time to part ways.
but oh well.
on the bike not starting there is a sensor that tells the bike when to light the spark. just a idea, but it seems you have done most everything i would do. but one question is can you get it to run on starter fluid? iv had motors run on that i just have to keep sparying it in. will tell you if you have a fuel problem or other issuse. just a idea.