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I'm hoping to get some help with my 2006 crf250x. The bike starts and runs very well cold. If I ride at a relatively mild pace the bike will start to hesitate and stumble then stall at about the 3 mile marker. With some effort it will refire and run poorly with some hesitation, then smooth out and run fine...... for a few minutes, then it stumbles again. If I run it hard and aggressive, it will stumble a bit, but won't die.
Mods-
Airbox opened
Pink wire
Jet kit w/165 main
Fmf Q muffler/sa
It ran fine after the mods but something happened since. I've checked for loose connections, vented cap, etc..... but I'm stumped.
Any ideas??

Welcome to the site !!

Did the bike sit for a few months before this happened ?? like over winter , etc ? , it could be as simple as old gas , or it could be a ignition break down (coil, CDI , stator) , or even a stuck or out of adjustment float , allowing the bike to run , but after it starts to drain the bowl , especially on rough terrain , that it starts the misfiring or behaving erratically , then when it stalls , and is sitting while your trying to restart it , then the bowl fills and your off again , not saying that is the issue , but its something to check , especially if the bike sat with Ethanol gas in it , and possibly gummed up the float needle causing it to occasionally stick and allow the bowl to drain , then slowly fill the bowl again if its stuck in a partial closed position

These are the first things that come to mind to eliminate , do you have a manual on the bike ?? , this will help in diagnosing , especially with electrical issues should that be the case , and will help with making sure your float is set properly as well

Thanks!
This problem started last year after I removed the shock for servicing. The bike sat all winter and last week I pulled it apart to flush the fuel bowl and check over any possible loose connections (I drained the carb before storage). A quick in spection of the carbs fuel bowl didn't reveal any tell tale signs.... wasn't gummy and the float seemed free. I'm going to pull it apart again today and remove the carb for closer inspection/cleaning. Since the bike hasn't left me stranded, it seems more likely a fuel related issue? My past experiences with electronics seems like once a cdi or felated fails they don't come back to life....

Sometimes it is true with electrical and sometimes not , sometimes when the component heats up it will break down (coils are famous for this) and when they sit and cool for even a few minutes , it will test or run fine for a while , not saying this is the issue , but its something to consider , CDI's sometimes have the same symptoms , nothing is absolute....

But I am thinking this is fuel related as well , but just covering possibilities here with electrical possibilities , have you messed with the Hot Start on the carb itself (not the lever) during testing and made sure its actually moving in and out and not stuck , as it can cause a lean condition that would be noticeable as the bike warms and leans further , or even a airboot leak or muffler being loose or mis-aligned can cause lean conditions (where the muffler and header meet or at the head where the header bolts up) , this can give lean symptoms , and can change as you ride because of the parts moving around and sealing then not sealing , the airboot where it meets the cab can be folded over and not noticed , take a flashlight , and look all the way around where the airboot meets the carb ...all are places to look into...........

Good to know about the cdi and the boot, thanks!
It seems like the problem would present itself easily, but so far not so much.
I'll keep digging..... these bikes are packed together tighter than a sardine can!

Yea , just be diligent and go over everything , 1 item at a time , and you will find the cause , sometimes you think you looked at something , but the next time you find you missed something the first time , and sometimes , your looking for 1 thing , and find something completely different that is causing the issues , these bikes are great when they run right , but are frustrating when things go wrong , and there are lots of variables that can give the same symptoms but be completely non related to what you thought it was , sometimes its something so simple you wonder how you missed it , or , you find something that has no logical explanation as to why it caused a issue or why it failed

Plugged gas cap vent? Next time it stalls, remove the cap and see if it starts back up. Your main should be closer to a 152, but that won't affect the issue you have now.

Check vent tubes from carby. Could be blocked or kinked after shock work.