Thanks for the reply, I am still investigating. The one thign I am trying to figure out is all the things that run from fuse 4 , from this thread http://www.xt660.com/showthread.php?p=214705 I see it may be

"There are quite a number of components take a feed off ignition fuse 4: starter relay (trigger), ECU, start inhibit relay (trigger), engine stop switch, instruments, immobiliser and cooling fan relay (trigger). The ECU, instruments and cooling fan relay are highly unlikely to be the issue, but it could be any of the causing the issue. "