KLR 250 intermittent problem
I've got an 04 KLR 250 that has had an intermittent problem since I bought it, and I need some troubleshooting help.
When I first bought the bike, the throttle response was terrible. Any quick grab of the throttle and the bike wouldn't respond and would just start to die. I thought it might have been a carburetor issue, so I cleaned the carb and adjusted the idle mixture screw. Things improved slightly, but then I had two circumstances where I was riding along and the thing just died on me in the middle of traffic. Both times it was warmed up when this happened. It finally came back to life after kicking it for a couple minutes, and afterward there was no sign of anything wrong with it.
A month or so later, I was riding on the highway on a cooler evening for about 30 miles with no problems, and then it started sputtering like it was running out of gas (but there was plenty in the tank). I pulled over and it shut off. I could start it after that, and it idled fine, but when I tried to rev it up to 4k+ rpms, it would rev intermittently and then die, and continue this sputtering/surging pattern until I closed the throttle. The bike would still function but it would start to die if I went much above 3k or 4k rpm. The next day I started it up and it was acting similar to the night before, but not quite as bad, and then after about 5 minutes
of riding the problem disappeared completely and I was able to ride it the remaining 50 miles to my house without issue.
I increased the main jet a couple of sizes and this had a fairly profound effect on the throttle response - the acceleration wasn't super strong but there was no longer hesitation. I thought I had fixed the problem until the other day I was riding it (low on fuel, on the reserve tank) and it started to die on me going up a hill. I was able to kick it back to life and then by the time I got to the parking lot at the top of the hill it died
again. I came back to it a couple hours later thinking it was just having one of its "episodes," but no matter what I did with the choke or the throttle position, no amount of kicking the starter produced even the slightest cough. I rolled it home, and even on the steep downhill parts where I was going plenty fast for a long bump start, I got nothing. Also noteworthy was the fact that I was having a lot of difficulty with shifting on the ride home without the engine on (not sure if that is significant). It took me about 5 minutes to get it into neutral and the shifting felt extremely harsh, like something was wrong with the mechanism. Then somehow that shifting problem resolved itself. When I finally got home, I was able to start it (having done nothing differently), although when I applied throttle it would die on me.
Any ideas on what this might be? I've cleaned the carb multiple times and it's never appeared dirty, although there was some buildup in the main jet but I replaced that. I've changed all of the fuel lines and the fuel filter multiple times. I've also changed the spark plug. I'm starting to look into the electrical system to see if it might be something with one of the coils, but after removing the ignition coil, I couldn't figure out which two points to measure the resistance between for the primary and secondary windings - the coil was different from all of the examples I could find online. Any suggestions would be extremely helpful.