Others chime in if they can duplicate please. I've done a number of runs over the same roads and can now reliably duplicate this problem, and depending on how I ride can reliably eliminate it or at least reduce severity considerably. This may explain why the Yamaha testers are having problems reproducing the surging on customer bikes.
First find a road that rises at least 1500 ft in elevation, with a lot of tight corners & short or no straightaways, requiring backing off throttle completely. Key is to ride the bike with very little throttle input, possibly barely cracking it open as you climb. RPMs between 2500 and say 4000. In other words, as if you own it, and are breaking your new baby in gently, enjoying the scenery, and you read the manual regarding rpm limits and so forth (and maybe are an old fart). [basically maintaining low manifold pressures for extended periods of time while climbing in altitude, and little-to-no throttle opening] Just cruisin'.
I have found I can pretty much make sure the problem doesn't happen or happens much less severity if while going through the above situation, I apply WOT between corners, blasting up to 8K rpms or so, braking hard, accelerating through corners, etc. Riding the bike like I don't own it, or like it's a sport bike, and I'm in a big hurry, or aren't an old fart in other words. [basically intermittentily providing periods of ambient pressure in the intake manifold while climbing]. Riding very aggressively in other words.
In both cases, stopping and shutting off the engine eliminates any hint of problems until climbing another 1500 ft.
I would be willing to bet that the owners who have reported this problem are also relatively new owners, who are riding their brand new $$$ bikes gently, through roads requiring or allowing little to no throttle. And I would bet factory Yamaha testers don't ride that way.
So to summarize, altitude + low/no throttle = surging problem. Altitude + agressive throttle = much less or no surging problem. If anyone else can reproduce this, please chime in. Note: I have a PCIII on my bike now, it masks the problem but does not eliminate it totally.