Ground issues will cause problems similar to what you describe when one device tries to ground through another. Start with the basics... remove all the plastic, tank, and seat and then remove and clean all the ground connections. Also check for wiring that appears too tight at loom splits and where the wiring is secured to differant areas of the frame, it can be damaged in those areas but not visibly.
But number one thing is make sure the battery is good. Batteries can turn to junk yet still have enough amperage to crank the engine. But there won't be enough voltage to fire the electronics. Take it somewhere and have it tested if you don't have a load tester to do it yourself. Or put a voltmeter on it while you crank the engine and watch the voltage. Most ECU electronics won't work without 12 volts where the old contact point and first generation electronic ignitions would fire with 9 volts. Low voltage will cause relay problems that can cause symptons like yours also but not as common. Good luck.
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jeff
'00 XC250 (mine)
LTS front and rear suspension, power valve cover, carb jet kit and rear chain glide, RB Designs head mod, BRP tall triple clamp, backyard foot-peg lowering conversion.
'04 EC250 (the kids)
(he can do his own mods haha!)
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