I'm not a tuning guru by any means, but I'm having kind of similar issues.
I suspect reeds or a weak fuel pump in my case. Partially rebuild carbs, but didn't touch fuel pump.
Swapping the vent check valve and eliminating fuel selector helped, but issue returned. Some say it could be my temp sensor, but my ski is an SXR.
On my other ski my running issues were resolved with a new ebox setup. Sometimes the CDI gets weird and issues can be hard to trace.
Sorry to hear, gremlins can be so frustrating!
I'm really really really hoping that it is the reeds because like I said, this issue persists with a carb with a rebuilt fuel pump, and some older carb off a blaster. Also I have changed every electrical component in the ebox to no avail.
I plan to swap check valves.