I have a 39 PWK on a LT250r. It has been bored 80 over, runs a V Force reed cage, K&N filter (clamp on style), shaved head, lots of porting, etc
I am running a DGH needle and 160 main jet. I think I am going to fatten it up a bit since it is about 20 degrees here right now. I have the pilot at one turn out, and the needle at 1 clip below center.
The bike tries to rip your arms off on the low end, blubbers through the mid range, and takes off again on top. I am thinking I might need to drop back to center clip on the needle.
Does this make sense? Should it clear up the mid range stumble I am having?

As I understand you, you have moved the jet needle up to the 4th position. Since the needle jet circuit operates in the 1/4 to 3/4 throttle position, I'd say you're a little fat there.