2005 crf250r rebuild

Hey Woody, like Motörhead said a smaller leak will force more fuel through the accelerator pump circuit. I believe your stock leak jet is a 70, a 55 or a 45 is common as an upgrade.

You said you bench tested before taking apart, I presume you also did that after rebuild. While testing did you have a 1 second stream of fuel roughly in the middle of the throat after the slide lifted ? no fuel should be hitting the slide. 
When / if you replaced the diaphragm did the new one match the old ? I ask because there are variations. The side of the diaphragm that faces down can have different length stoppers. The longer the stopper the less pressure the fuel will flow. In this picture you can see the different lengths.

All that being said, did you try riding it ? Might be worth it before getting overly concerned.

Not much vacuum on these things to handle an idle to full throttle whack without a stumble. I think a better test would be from like an 1/8 or so to full throttle. 

Bogging off idle with a quick twist was a common problem with the old carbed 4 strokes.   One of the ways we combatted the problem back then was to wire the accelerator pump linkage together so there wasn't as much lag.    Some people were using an o-ring, others just used safety wire.

Even the best-tuned carbureted four-stroke can be made to cough/die/bog when not under a load. Whacking the throttle on the stand won’t tell you much.

Nice mod!   I used to just run the idle high, seemed to help a lot from what I remember.

What color was the smoke upon startup and did it only smoke the first time you started it after the rebuild?

The leak jet only comes into play when you turn the throttle quickly. If you run through the gears and gradually increase the throttle does it run smooth?

Do you have a manual for the bike? If so there should be a jetting table in the manual, I'd use those settings for your environment as a baseline setup.

Tough to help diagnose without more info, smaller leak jet wouldn’t hurt but Sounds like stumble is in the zero to 1/3 throttle opening.

Were you going to zero throttle while shifting ?
Did you try adjusting the fuel screw on your test ride ? 2.25 is on the edge of range, try going up one size on pilot or check it for any blockage.

What needle and clip position are you on ? Could raise needle / lower clip position.
What rebuild kit was used ? 
Did you clean/replace hot start plunger and choke ? 
Does it start easy ?

You can access a service manual at http://owners.honda.com/assets/ownerlink/model/own_man/powersports/2005/2005_crf250r.pdf  to check for carburetor tuning and adjusting details.

Im sure you already did this but check the manifold and air box boot for any bad connections and for any cracks, don’t need to be trying to tune around that. 

RedRocket is on point here.

I would check the obvious first - Choke plunger, Hot start plunger, and make sure the fuel screw located at the bottom of the carb is there and set at the right number of turns out.

I bought a used bike once that the fuel mixture screw had completely dropped out of the carb, but still sort of ran somehow if i kept the throttle cracked.    The screw is hard to get to when it is on the bike, and aftermarket companies made a killing on extended thumb screws back then.