IMO, you're dealing with an inherent limitation...the stock valve size. Subtracting the area obstructed by the valve stem, there's not much more cross-sectional area possible, i.e. open to airflow, beyond the stock 22mm port diameter. Not saying that there's no potential gain lurking in this casting. I am saying that virtually all of it would come from changing the port shape. Unfortunately, there are tradeoffs; increased port volume means decreased flow velocity, along with the unknown effects on turbulence and swirl, of the incoming charge, as it enters the combustion chamber. The expected side effects would be loss of efficiency, as manifested in mpg numbers and low-rpm hiccups...like you're getting. I'll take your word for it that this is a transient rich misfire, despite the fact that it strikes me as a transient lean stumble. You're there and know your way around carburetion while I'm ~900 miles away, behind a keyboard. If you are correct, then there's a high probability that fuel is puddling in the intake, at low rpm...due to undesirable turbulence.
Speaking in theoretical terms, the ideal would be a raised intake port, with a uniform 22mm ID. That would mean welding-up the port floor by the same amount its roof is raised. With an extra 4mm of bore size and ~30% displacement increase, there should be enough vacuum to compensate for the port volume increase and likely any loss of swirl that was engineered into the port configuration...in terms of peak hp & throttle response. Unshrouding a valve is a classic method of gaining airflow (and with it, hp) what's never discussed is the bottom line impact on efficiency. The acid test...and you're the one person who could do this...would be a side-by-side comparison (literally, this bike & your stock Nice-powered bike) of fuel consumption numbers. To date, I've yet to see a big-displacement tune that didn't slurp fuel at a disproportionately high rate. (FYI, I'm talking about normal road riding, not 60mph+ sustained.) That's a textbook manifestation of reduced efficiency.
Since this is going to be a serious tourer, efficiency (fuel consumption, throttle response) and simplicity are part of the equation, imho. I'd be thinking in terms of a 22mm carb, minimal work on the intake port...with the goal being uniform, high-velocity, airflow... and the bigger port changes on the short-turn side of the exhaust port. Best, educated, guess is that this motor is ideal for a VM22, fitted with a #25 or 27.5 pilot jet and somewhere around #210 main. With this displacement & head configuration, I'm not sure that the more refined MJN22 would make much of a difference and the VM22 is dirt cheap.
FWIW...