i just bought an 88 250r that has a FMF pipe, K&N with lid removed, ported and polished and a keihin 39mm. It stutters/sputters when I smash the throttle until you get to about 3rd gear and then she is gone. So i think it is running lean, and the gasket off the manifold to the reed cage was a little wrinkled so I replaced it and it is a little better but not completely better so I think I am going to go up a jet size> good thinkin??

 

pull the pilot jet and see what size it is...get a couple more 1 size up and 2 sizes up, give them a try.
you might try messing with the needle a bit too, raising the clip and lowering the needle leans it, while lowering the clip and raising the needle richens it...

 

Your running rich, not lean. Drop the pilot jet in size.