If you're blowing the main fuse, you have a short-circuit to ground from switched + 12 VDC (BROWN wire), seems to me.
I'd have to chase it with a multimeter and a wiring diagram (Googling, "KLR650 Wiring Diagram"), were I in your situation.
Regrets I can offer no more useful help; maybe another forum member can offer some worthwhile advice, probable diagnosis and cure.
Generation 1 engine oughta run anyway, ignition ON, kill switch in RUN position, bump-started.
Last edited by Damocles; 09-03-2013 at 04:54 AM.