I've never had to deal with a failing CDI, but it is possible for one to become weak and intermittent as it heats up . You seem to have pretty much eliminated everything else . Hopefully you can borrow a good one to try before putting out the bucks for a new one . Friends of mine who had CDI problems had them fail completely when they went. Like anything electronic though, a component can get weak or out of spec and cause problems.

Btw they updated my quote since they sold off some accessories with the smaller trailer, seems I'm still about 6k (5800) so it just doesn't seem as good of a deal anymore, which is partly why I'm looking at shipped from Utah option....if you were me what would you look at doing?

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Have you had a chance to try another stock carb on it ?. It still sounds like a lean burn problem off idle.I'd look again for a clogged passage or a small missed drilled hole in one of the jet tubes . Make sure float level is right and no crud is coming from the tank to possibly restrict fuel flow .. Is the diaphragm good /new and working as it should? Is the spark plug new or known good ? Some plugs can be fine at idle but under the higher pressures when throttle is opened can cut out or be intermittent .

Sorry for the long update, since I posted this I blew the transmission out of my race bike, which ment tearing down the 450, while trying to rebuild my camper, and getting ready for a hard enduro competition on the one weekend that wasn't a race weekend. I have yet to mess with the bear tracker, however I did take it to the last event and it basically stopped running. Stumble is so bad it barely has power to pull itself, choke in, 1/2, out doesn't matter it wouldn't run. So I'm hoping to get around to tearing it down in the next week or so, I will still update this page when I figure out what's up.

You can slide the whole tent out and flip the gates vertical to use as a utility trailer. Mike

Any chance the fuel tank has junk in it ? Maybe remove the petcock (gastank valve) and check the screen and inside to check for junk and that it’s not starving the carburetor for fuel? Esp since you said when you start moving the bike around it gets cranky.

I'd check for loose or corroded connectors in the ignition circuits first since it started after bouncing around . Check the voltage from rectifier to battery under idle and revved up. If you can borrow a compatible CDI box, you could try swapping it out. There is the service manual for the 1998 YMF250 in the downloads section of the forum . It will have all the resistance readings for the ignition components should you need to check the stator, pickup coil and ignition coils. Most likely the readings would all be the same for the 2001. Very little changes from year to year for the same series motors. Check components cold and warmed up. Sometimes they break down when hot but are fine cold. One tool that isn't expensive but is often overlooked when suspecting spark loss under load is an inline spark checker to see if the plug is firing properly under load. Here is an example of the spark checker https://www.harborfreight.com/90-in-line-spark-checker-69023.html