Well, the first thing to figure out is if hers has the same main jet size as yours. Both bikes would normally have a 126 main jet. My 2010 has a 126 and the only time I change to a 122 is when I plan to be above 8,000 feet for a few days. The pilot jet has little effect on the mixture above half throttle, so that is probably not it. I set mine at 2 turns and never changed it. I live at 5,700 and normally ride between 4,000 and 9,000.
I HAVE experienced missing, or I would call it stumbling, which is a little more subtle than a real miss, at full throttle going up hills. It is intermittent, and never occurs in any lower gear than 5th. IF I lived in Nederland and NEVER went all the way down to Boulder, I would probably leave the 122 in all the time. Problem is, coming up the canyon, you are going to be too lean winding it out to avoid being run over! ( Boy, I LOVED that road!) The 126 is just right from 4,000 to 7,000, and will work all the way to 12,000, but not WOT in 5th.
One thing to check is get her bike to missing at full throttle, then cut the throttle, clutch in and coast to a stop and pull the plug. If it is pretty dark, the carb is too rich. If it is an ignition problem, the plug will look fairly normal. Ignition problems almost always get worse under heavy load. A 2007 should not have any ignition problems at 4,600 miles, this is pretty rare on the newer bikes, so I think it is much more likely to be cab related.
As for your stubby, I'd grind it a bit narrower so you don't bugger the threads in the hole. If you loosen the clamps, you can turn the carb up to 40 degrees to the right without having to detach the throttle cables. Then you can see what to do.
At the time you DO decide to remove the float bowl, get some JIS screwdrivers FIRST! Then replace all four bowl screws with SS Allen head bolts. Or you could take in in and ask the mechanic to just loosen the screws (provided HE has JIS drivers!) so you can replace them. This will make jet changes a piece of cake. Have a careful look at the carb pictures before and during a jet change...parts can fall out! You want to hold the main jet holder with one wrench while unscrewing the jet itself with another, that way nothing will fall out. You will not need to remove any other parts to do a jet change, just make sure the gasket is seated in the bowl recess, and only tighten the Allens moderately with two fingers.