kz250 face falling

I've seen a couple similar threads but I don't seem to have the exact issue and pulling my hair out so here goes;
I have a 1980 CSR250 (KZ250) that I totally rebuilt from seized engine to working moto. Sort of. New piston rings, cylinder was honed, Valves were lapped and adjusted. Stock electronic ignition. Box removed and air pod and new dime city cycles shorty exhaust installed. I'm at ~4000 ft elevation, stock jetting is 35 pilot, 68 primary main, 98 "secondary" main.

The issue: engine will start easily with choke on, idles very well and smooth, no misses. After say 30 sec I can let the choke off and it will idle at a lower RPM, but maintains, again smooth and no misses.
If I roll the throttle fast or even very slowly it fall on its face, acts like the engine is working very hard if I go slowly. I can let off and it will idle again.
If I have the choke on again, it will idle faster and I can roll the throttle or punch it and engine accelerates but still acts like its working hard to do so.
With the change of the air box to the pods and from the megaphone to the shorty exhaust I assumed the engine would be breathing without nearly the resistance and thus would be running lean. I got some jets (70 to replace the primary main 68 and 115 and 125 to replace the secondary main 98) but these make zero difference.
I have cleaned the carb and all the orifices, blown air through each passage to make sure they are clear. Tried to get the plug out for the idle air mix but was proving difficult so I left it since it idles fine (I feel this could still create issues throughout the RPM range though).
The tank petcock will flow freely and generously. I adjusted the carb float to what appears to be adequate level
I know there are other details but I'll throw the video with it as a better-than-words description. It is running with choke off, trips when I roll the throttle and works hard when I slowly roll. I then put the choke on, RPMs go high and I can roll the throttle with engine response.
I would think bogging/dying means it is too rich which is supported by the spark plug-very black-- but it just doesn't make sense since the modifications would make it lean and it runs better with choke on which also means lean. Instead of blabbering more I'll leave it to the video. Thanks for hopeful solutions! (couldn't attache video so I'll post this much at least and get video on soon as I can)

The video

Also, I can cover the air pod with my hand to restrict air flow (simulate if the air box was still on) and there's not really much difference if any.

No expert here, but check and lube the ignition advance.
Good Luck

Its a good thought but its an electronic ignition (based on pulses from flywheel vice the mechanical weight advance on the side of the camshaft cover). Also, it revs when the choke is on which makes me think that circuit (the electronic advance) does work.

I've owned a 250 and can give you some suggestions,

1st and foremost - Running pod filter on that finicky ass CV carb is going to be a nightmare, put the box on it.
Next, the lil 250's we set up pretty lean, but I learned they are incredibly sensitive to jetting changes, I would only try messing with the pilot jet. Leave the mains alone (leave them stock for now) until it runs better. Again with a pod filter on it going to be a total crap shoot. AND then there's the exhaust too, you may want to be looking at a new carb, that CV is very touchy.

The ignition is fully electronic, IIRC idle is 20°BDC and 4,000 rpm should be °40BDC.
Usually the ignition either works or its completely out.

A lot of people miss the fact that even though the 250's are only 19hp they are actually a pretty well tuned engine, messing around with the air box and exhaust is going to be some work to get it running right.

Is the cam off a cog? Double check your timing marks, that could be a possibility too. But I doubt it would run at all... still worth a look though.