I have a 88 250R that stumbles just as you give it gas but after the stumble once it revs out it seams to run fine at higher RPM. I took the carb out and cleaned it all up and checked the Jet sizes it was all stock. I thought maybe it was the LRD pipe on it so I took that off and put a stock one on but it runs the exact same way. It starts up with one kick and when revved in nuetral it seems to rev just fine.

Any help would be appreciated!

 

An engine that doesn't run good will be able to "rev out" when sitting in neutral.
It sounds like you're starving it for air and/or fuel.
Start by opening up the air box. Do a plug chop.
Just 'cause you have stock jets doesn't mean it should run good.

 

I agree with trapperb1.
If you have the same jets, but have changed pipes, etc, chances are you may be too lean.
If it revvs out ok at full throttle, you may be lean on the needle.

A slight hesitation before taking off often is caused be too lean of a condition.

You might also want to play around with the pilot jet (go up and down) to see if this is what is causing you the problem.

At what throttle position is the hesitation occurring?

You can do a plug check (as stated before).

At half throttle, you will be checking the needle position. At full throttle, you will be checking the main jet.

Have you ever done a proper plug check?