A certain amount of spitback is to be expected in a piston-ported 2-stroke engine. Running with the airbox off makes this a bit more pronounced, but even with an airbox, the inside of the airbox will be wet from air/fuel being shoved back through the carbs.
You are also right, the "choke" system on Mikuni VM carbs is an "enrichment circuit" not a choke. You could have a plunger hanging open, but if it is idling fine, I would not expect that to be your problem.
The air/fuel mix at idle to 1/4 throttle on a Mikuni VM is controlled by the pilot jet.
Air/fuel from 1/4 to 3/4 throttle is controlled by the needle jet/jet needle as it meters fuel from the main jet.
Air/fuel over 3/4 throttle is controlled by the main jet (with a little fuel coming from the pilot jet circuit).
When you drop the main jet size to decrease fuel delivery, it affects the midrange and wide open. Dropping the jet needle further into the needle jet will give less fuel from 1/4 to 3/4 without reducing top end fuel delivery.
To figure which circuit of the carb to work on, identify where your problem is; idle, 1/4 to 3/4, or above 3/4. That will point to the correct circuit in the carb.
Where are your e-clips set now? Try going one notch higher (thus lowering the needle into the jet) and see what happens. Can't hurt, and its free

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2007 RMK 700 155", 2008 RMK 600 155", 2006 RMK 600 144", 95 Prowler 550 2-up, 1990 Indy 650
RIP, destroyed by fire 1-22-2008

04 RMK 800, 05 RMK 600, 02 RMK 800, 97 RMK 700
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