Squeaked out of work a few minutes early yesterday and went up to the Parkway. Bike ran great, but you can definitely feel a rich dip at around 4,500rpm once you're above about 5,000' elevation. It pretty much goes away once you drop below 3,500' or so though.
In the end, I think I'm just going to have to live with it. Maybe I could make a minor adjustment with an adjustable needle, but I really think I'm just going to have to ride around the spot a bit. you only feel it when you're accelerating at wide open throttle. With the new bullshit chipseal the NPS has paved large sections of the Parkway with, you don't want to be pushing your bike up there anyway.
Our Mikunis are not self compensating. From personal experience, significant altitude changes will cause the issue you're experiencing. Not much you can do from a realistic point of view, other than using an adjustable needle as you mentioned and setting the "clip" for the best results. The frustration is having to remove the carbs to do this but with the 5-slot needle a happy medium can be found. This depends on where you're riding and the altitude differences involved.
I tried to find an article that I read some time ago (couldn't locate it) which stated (academically) that given all of the needles and jets available - the combinations numbered 10,000 !!!!!!! This included straight and dual tapered needles. You'll spend less $ on a Straight-jacket ! Then of course there's the affects of Density Altitude which are Temp./Humidity/ Baro.-pressure related ! On a trip many years ago, I had to stop half way up a mountain pass to lower the needle height, to keep the bike running. Thanks to a kind farmer, I had the opportunity to do this in a barn, out of the weather. Not the ideal environment but had no options. Ah, the excitement of using a piece of car-board as a work surface and praying that "something" didn't flip-off into the dirt! Couple of hours later I was back on the road with no further issues.
I still use the middle (#3) slot for my riding area which is 1140' A.G.L and have found that one slot up or down just doesn't work. Either too lean or too fat. Don't do much long distance/mountain pass rides anymore but would expect to feel the affects, as you are.
1980 KZ 1300 sr# KZT30A-009997
Always High - Know Fear !