Motorcycle Repair: 1998 XR200R will not start, mud puddle, xr200r

Question
My son's xr200r was running fine a few weeks ago-until he submerged it in a huge mud puddle. I actually got it running after the mud by draining the float bowl out on the trail and bump starting it. It was spewing water out the exhaust. My fears were confirmed when we drained the oil and found water in the oil-milky color. He pressure washed it and then it would not start. I put fresh oil in it, new spark plug, drained the gas and put new gas in. Cleaned and oiled the air filter. Still would not start. So, I pulled the carburator and cleaned the idle and main jet- both were clogged.I thought I had the problem solved but still it will not start. Seems too easy to kick over but don't have a compression guage. I got the shop manual out and started checking wiring-spark is there but seems weak. The ignition pulse generator ohmed out at 96 and is supposed to have a value of 460-520 ohms according to the shop manual. The decompression lever does not work but does not seem to be engaged(in other words-holding a valve open). Are 98 XRs prone to any problems? This bike was well used when we got it and I had to put a clutch in it as soon as we got it.THat's probably when I screwed up the decompression lever. The rest of the electrical components(haven't checked the alternator)seem ok by the multimeter except the ignition pulse generator. This is probably an expensive part that cannot be returned. I am to the point of pulling the engine out of the frame and tearing into it.Thought it would be ok since I got it started after the mud puddle but water in the engine may have done some damage. Any ideas you have would be appreciated.

Answer
Hi Michael,

Water can compromise the electrical system by entering a multi-connector and shorting a circuit. I like to use dielectric grease on all connectors to prevent this. It may be several day before water evaporates from a connector. You may or may not be experiencing this problem.

I would start with a cylinder compression check and possibly a leak-down test to determine condition of combustion chamber's sealing properties.

Have you veriied that fuel is flowing into the float bowl? When you cleaned the carburetor, did you clean all passageways and jets? Remember, every pinhole inside the carb is critical to proper operation.

Variations exist between meters used by us, and the meter used by the factory. Vaiables include temperature, wear, meter zero and battery condition, to name a few. The pick-up coil's winding should be ok if you have continuity.

Keep me advised of your progress.

Respectfully,
Mark Shively
mshively1@woh.rr.com