Supposed to be close to half an inch, Well 0.40" or 10mm below the intake port. (just tried on a spare engine to see. It actually lined up with a scribed line on the rotary valve surface.) Could be one tooth off if its closser to 1/4 inch.
But that's something else and would only contribute a little to this problem. I was wondering if you were really close to the port.
When you get it up in the rpm's do you have to keep the choke on or can you let it go and stay in the high rpm's with the throttle?
Also, if you give the throttle 3-4 shots (to try and flood the engine using the accel pump) can you get it to respond at all to throttle for a second without using the choke?
If its a low end problem, as in pilot/pop off/acell pump, not contributing at all, using the choke would make the main jet kick in and that's what your running on.
Since it does run on top end, that mean's there is fuel in the float chamber that the main jet is pulling from. I wonder if maybe there is still something stuck in the pilot circuit.