Pulling the choke our creates the added vacuum (pressure) to open the needle valve and send fuel into your engine. You have to look at this in a few different ways. First, and something you touched on, is the transitions. When you first start the motor, vacuum from turning it over, pulls fuel in from the low speed/idle jets. If you rebuilt the carbs, when you sprayed cleaner through the low speed jet, you should have seen cleaner spray from 3 holes on the inside of the carb, one on the engine side of the throttle plate, the other 2 on the outside of plate.
When you start to increase your throttle, you transition from the low speed, to the high speed. During that time, your fuel is coming from both. When you go WOT, you'r only getting fuel from that high speed jet, which is really not adjustable. There is a black cap that covers that screw. It is basically a bypass around the jet, not an actual jet adjustment.
Like I said, there are a few things at play here. Because you just rebuilt them, I'd make sure they both pop off around the same pressure. If you have one that pops off at 5 psi difference from the other, that can cause bogging. Also, your sync bar. After the rebuild, make sure your MAG carb, which has the idle screw, is backed off all the way. That will ensure both carb throttle plates are closed. Then, set the sync bar up to the ball. If they align well, then pop it back on. If the knobs look to be off, then adjust that bar to meet that requirement. After your satisfied with it, then turn the idle adjustment back in 3 turns.
Last, when you do get it running, with it idling as best you can, or even if you have to idle the engine up a bit, let it run like that for a few minutes, then pull the kill switch. As soon as you kill the motor, pull the plugs and read them, see if you got a plug that's dry, or running lean. That'll help you see the problem.