Well, you guys certainly seem to know your stuff. I did spend a butt-load of on my R1 ($2,000 titanium exhaust- to eliminate the OEM exhaust flapper valve, Power Commander, and mapping), to repair about a 20 horsepower hole in the powerband at about that same point (centered at about 7,500 rpm).
Maybe keep the stock stacks then. How are you guys cutting the airbox? Is the Gen II airbox like the Gen I airbox inside?
I've done simple stuff like port matching, thinning down valve guides, removing air injection bumps, blending to remove the "step" at the valve seat, and polishing on piston engines, but any substantial deviations from the original port design would probably be beyond me.
I do have some reasonably successful (as defined by the 66 foot dyno at the end of the drag strip) experience with huge changes to the port design of rotary engines. I learned at a race car fabrication facility that had an engine dyno. It was all done by setting the main port timing with a known template, drilling the auxilliary "bridge port" with a template, and then porting everything by hand, using my eye, a strong light, and only basic measuring. No flow bench. Mine worked about as well as anyone else's porting, but we're talking about two different animals here, and I don't want to screw it up.