Well if it were an XR, I'd say that the valves are tight - have they been adjusted recently? Another thing that I had heard about earlier models of this bike is that if it fails to start within a reasonable amount of time, then turn it off for 15 seconds to let the ecm reset.
If it were me, I'd start by adjusting the valves, clean up the ground wires on the frame and make sure they have good contact and check the coil.
jeff
p.s. Nice pics of your bike in the photo gallery...
