(Mark, read the bottom line before tearing things apart, if you would.

)
Yes, this re-jetting over the internet has been fun. And yes, the bike is not getting the results that other 1000's with similar mods do.
This bike started out with bad gas mileage and still gets bad gas mileage.
As for the jetting, in my defense, I said from the beginning the stock needle doesn't work many times, especially with K&N's and I prefer jet kits. I also said to put the stock needle in the 5th position, if it had any chance to work at all. I still stick to my main jet selection because it's certainly "ballpark" by past experience and wouldn't cause these problems on any other 1000 I've jetted or helped jet. The pilot circuit SHOULD work well with just pilot screw adjustments and the air screws adjusted for highest rpm.
Everything else... spark, compression, valves, clean/correctly adjusted carbs, etc, Mark says is good.
But what we have is a bike that's passing fuel, though the most commonly used circuit, the needle circuit, is fairly close according to the plug photos.
However, now the bike is giving rich reads on the plugs?? With no needle change and only a leaner main change?? Makes NO sense. He has played with the valve clearances since the leaner reads though.
All I know is if the bike was here I'd go through everything and suspect everything.
Last I saw, the needle was as close as the stock needle will get and was lean at 2/3 if anything.
The main, as Mark just said, is now too small and the bike's top end is suffering. The smaller main will help MPG when on the main but when the top end is suffering this is an obvious sign you've gone too far. On a properly running bike, the main is not the cure for these problems.
With a pipe and K&N pods, the stock pilot circuit works fine almost every time after screw adjustments. Sometimes a 17.5 pilot jet helps with decel' pop and cold start "spitting" out the pods, but the larger pilot sometimes creates rich related problems and you just live with the less troublesome decel' pop.
As I said earlier, at this point I would start the inspection with the pilot circuit and the needle jet. Pic's with the parts next to a ruler would help. I'd like to see how the float levels were set, etc, etc.
PS:Mark, if you now chop tested the plugs at full throttle, 1/3 throttle, and at a steady 35 in 4th gear (in that order), that would help too. And, where is the sweet spot on your air screws now?