i had an 88 wr500, 2 days before the new owners were picking them up, i decided to run them and make sure everything was o.k. I left the battery terminal a little loose, ski was running, then just quit. cdi was fried. Good chance you cdi is bad, but first i would bypass the stop switch. Check the coils,grounds,ect
also, get a manual and you can test it.
I ended up buying a junk ski and swapped out the cdi
i had the exact same problem with my 92 wr and the shop told me it was probably the cdi....i did my own investigation and found the little stop switch thing for when you fall off (sorry don't know the proper term haha) wasn't disengaging properly...sprayed some cleaning solution in there and now it works perfectly!!!