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Discussion Starter #1
New owner of a abused 2009 ex500r with 16xxx miles, before the problem I'mt currently facing I'll go over some of its history so ya'll can have an idea of what could possibly be wrong with it, whats been done/what still needs to be done. When I bought it for 1800, like the sucker I am, guy said he had a third kid on the way and I felt bad. When I drove it home it would only hit 55mph, after getting it home, I noticed the airbox had no top, and the filter was held it place with squares of foam, I bought a top for the airbox and took the filter out, but ended up putting it back as it honestly looks brand new, but plan on getting a K&N should they ever come back in stock, drained the gas tank and looked inside it, there was so much rust it sounded like sand sliding around, so I put vinegar and rocks in it to clean it out, then when it was still incredibly rusty I tried electrolysis, after 3 days of being on a current it finally stopped bubbling up new rust, drained it, dumped boiling water in it, shot it with a heat gun to make sure everything was super dry, put the old petcock back on and filled it to the brim with gas, Rebuilt the carbs, synched them, and set them both to 2-3/4 turns as I've read factory is 2-1/2 and that tends to be a bit lean for people. replaced the spark plugs, changed the oil and filter,and plan on doing the valve adjustment this week, then tuning the carbs to what the old girl really wants instead of just setting it to something it runs with.

The problem I've come across the more crucial one first is when I was driving back from my fathers house, I was hit with torrential rain, at first the bike was fine but when I was near home after ~30min of riding, the bike began to run very poorly, now today I was hit with torrential rain, the bike ran fine at first for about 3-4 minutes, but now it just cut off like I had chopped the throttle closed and steadily went down from ~8k to 0 on the highway as I was going about 70, when I was able to get it started again I had to baby it around 3k then I would rev it to ~8k and it would die, but sometimes it wouldn't, I could pull it a couple feet giving it just enough gas to get it to 3k, then it would die, if I sat with it in neutral it will rev up fine...sometimes, then it will die when I let off the throttle, or sometimes it will bog at ~5k once it gets over the bog it can rev to redline and if I let it down slow it will run, until I let the gas off completely, I could occasionally get it up to ~30-50 and ride normally but then it would die again, I've had vacuum problems before where the hose from the petcock comes loose from the carb as the tube I was using was silicone and eventually expanded too far to actually seal around the petcock, but they seemed fine. Once I was able to pull it under a tree and it wasn't getting rained on so hard it was able to eventually even out and idle rather fine, and I was able to rev it to 5k without it bogging, once I took it out from under the tree the problem came up again, and I ended up having to put it in neutral, start it, pull it a couple feet, until I got home.

The less pressing problem, when I first start the bike up and come to a stop the bike dies sometimes, but it also does this very rarely when it is already warmed up, if I have come off the highway and chop the throttle closed, and start braking to take the off ramp I can watch the tach go from 8k - 1/2k then back up to it's idle at 1.2k if I do this when the bike is cold and simply chop the throttle closed it will often die, and will sometimes start with the clutch pulled in gear, but more often I will have to switch it to neutral with the clutch out to start the bike, and when I clean the carbs ~every week I am still getting alot of the fine powdery rust in the bowls, but rarely are the jets clogged, sometimes they are obstructed but not fully closed, is the tank the culprit of my problem or perhaps it is that the cams haven't been timed in 15k? Sorry for the wall of text.
 

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Are there any filters on the fuel line or did you use the drip in filter in the carbs? Search fuel rail filter if you didn't, would be a good investment. You didn't seal the tank correct?
 

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Discussion Starter #4
Yes I am using the rail filter that is recommended, and no I have not sealed the tank, as most here seem to recommend against it.
 

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If it runs under a tree, and immediately breaks down on contact with water, I would suspect something wrong with one or both ignition coils.
Happens at the car wash on some bikes, coil wires get wet, bike won't start or run right. Troubleshoot: warm up bike in driveway,
verify revs okay, then turn on garden hose directly at spark plug holes, see what happens.
 

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yeah runs in the dry problems in the wet sounds like an electrical issue. water and electrics don't mix. could be water thrown up from the front wheel soaking the engine bay. you could try dosing all the under tank electrics with ignition sealer (comes in a aerosol can) and make sure the plug well drain holes are clear.
I had the same issue years ago with a Honda 4 cylinder ran fine in the dry but as soon as it started raining it got a misfire dropping cylinders one by one until it stopped. leave it under cover 30 mins for the engine heat to dry it out and it ran fine again. never did cure it just stopped riding it in the rain.
 

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IMHO possible overlapping issues? requiring multiple checks, actions to take:

Spark Plug Caps/Wires:
disassemble, assure presence of spring and resistor, wipe clean the goop from the plug cap inner/outer walls, retighten the brass lugs
trim the spark plug cable ends to assure full wire contact, replace any broken, split rubber wire/coil/spark plug capseals

Airbox:
replace any missing components you mentioned. Assure the associated crankcase breather J hose is present and connected.

Petcock:
both screens present? inner ports clean and clear? (they have a tendency to pick up fuel/ethanol corrosion, leading to the most famous vacuum petcock failure)

Tank:
POR-15 tank sealer saved my Ducati tank from rust tendency (prolly done10 years now, intact, no issues since)
Rainwater water infiltrating fuel? Tank cap surround drain is operational? cap seal intact? both worth checking

Carbs:
drain each bowl into a catch container, inspect for presence of water If so, take appropriate action...refer back to tank/airbox infiltration.
 

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Discussion Starter #9
I apologize for not updating today, and I appreciate all the replies, the only thing I was able to get to today was checking the j hose, and found the end that goes into the airbox was secure, but the part that goes into the crankcase was simply touching the top of the hole it goes into, I started it and noticed it SEEMED to idled better, and as I am in a apartment I do not have a gardening hose I do however own a 10gallon bucket and drenched the sparkplugs while it was running with no difference in idle, I am confused as to why the j hose would help the idle as from my understanding it simply feeds air from the crankcase back into the airbox for emissions reasons. Is the thinking that the suction could draw moisture into the airbox, or more simply water got into the crankcase from the insecure attachment? Would that little "assumedly" amount since the hose wasn't fully dangling amount be enough to cause the bike to die on throttle?
 

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I have a possibility which has not been mentioned.
It is not uncommon for some of the hoses to get routed incorrectly by mechanics who weren't paying attention when pulling things apart. The 50 state models with the evap canister and associated vacuum tubing are the most common culprits, though it's still possible on the 49 state models. I have encountered this issue on both the EX500's and the EX250's (the older style). If the fuel filler drain line (the line that comes out of the tank right under the front of the seat) is routed down into the carburetor vent (the upper plastic tube connecting both carb bodies), you will get water in the fuel and your bike will run like soggy garbage. If you have a 50 state model with the fuel evaporative stuff (if there are two vacuum lines coming off the front upper right underside of the fuel tank, you have a 50 state bike), there's a variety of ways to route the hoses wrong which will result in water entering the carbs and the same resulting terrible running engine.

Remove the fuel tank and check your upper carburetor vent tube. If there's any hoses attached to it, remove that hose, rotate the vent tube so it is pointing directly down and leave it. If you have a 50 state model, I know there is a walkthrough on how to remove all that emissions evap stuff, I highly recommend removing it. Then, check your fuel tank filler drain under the front of the seat. You can either run a hose down to the bottom of the frame or leave it with no hose, though I do recommend running a hose down to direct the rain water away from the electrical cables running off the generator under the frame right there.
 

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^ 50 state bike?
Wouldn't that be a 1 state bike?
 

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A few thoughts in random order: Does it still have a fairing? Sounds like rain water/spray/mist could be infiltrating an electrical connector toward the front of the bike - maybe even the ignition switch and/or harness. Check the right handlebar switches as maybe the kill switch is getting wet! The fairly quick and easy way is to unplug all multi-connectors and check the condition of the brass connectors. A little brake or electrical contact cleaner and good old fashioned pipe cleaners will brighten them up. Snap them back up and silicone spray them to keep water out.

If it still does this - again, only in the rain - when the bike stops, put on some mechanic's gloves and pull the plugs. Crank it and check for spark. If both spark, then it would point toward fuel, but that makes no sense. If neither sparks, then check the wiring harnesses at the ICU and the coils. If only one sparks, then it is probably rainwater fouling that plug lead or the wires leading into that cylinder's coil. Maybe take a can of computer duster along and spray those contacts and see if it makes a difference. If it does, then water is simply causing a short to ground when it is raining.

Make sure the coils' high tension leads (plug wires) are making good contact at both ends. It is very common that the ends of the wires which slip into the coils simply and are held by a threaded collar need to be trimmed 1/4" or so and reconnected. Silicone the heck out of the plug wires, as that electricity is much more likely to arc to ground before it reaches the plugs.
 

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^ 50 state bike?
Wouldn't that be a 1 state bike?
50 state means it passes initial emissions requirements in all 50 states. 49 state bikes (cars too) passed the initial emissions requirements of all states except California. Other terms used are California legal or C.A.R.B (California Air Resource Board) legal; Federal emissions is the term used for 49 state anything. The caveat is that now for the last several years, New York has been requiring all new vehicles sold to be California legal. Any vehicle before after a certain date which came standard with California emissions equipment must retain all of that equipment. Motorcycles still don't have emissions tests I think anywhere in the US, so this only applies to new motorcycles being sold.
It's not uncommon for companies to just sell 50 state cars in all states so they don't have to make and ship different variants of the same vehicle.
 

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^ Thanks for clearing that up for me. (y)
 
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