Tony, here's what I experienced yesterday when my modified airbox developed a leak and caused everything to go wicked-lean in the pilot circuit.
I experienced everything you had until I chased the problem down to a failing seal and reset it all after going to all extremes on the screws. Too lean and the bike would stall, too fat and the bike would bog till on the needle...
-The main and the needle are the least sensitive to these changes (especially if you've already dialled them in according to FP). You'll notice that 1/4 throttle is what is the most affected (ironically the most often used throttle position).
Once you decide what setup to use on the intake and exhaust side of things is when you'll want to dial in the pilots. FP is right when they say to set your idle to spec and make sure the screws can hold it. The other circuits will follow pretty seamlessly. Make sure the bike is at operating temp when doing this.
-Once your screws are set and you're done, resynch everything. This affects how well the carbs react to throttle, closed or open. Also, changes to your idle screw will affect synch as well (at least what I've experienced).
I spent a couple of hours messing with this yesterday and endt up back at the settings that I had originally started out with. I'm happy I didn't get crazy and started going after the main and the needle because after I marked the grip and controls with throttle positions, it really helped me dial it all in and find the trouble spots. Using the combination of both those websites is a big help.