According to the article Mike linked above "the pilot circuit affects the entire throttle range. When you are at full throttle, the main jet is the primary fuel metering device, but the pilot is still delivering fuel as well, adding to the total amount of fuel that your engine is receiving.", so my thought is that since both bikes sputter up to WFO, the plugs are black, and to still err on the caution side, then I should start with installing a smaller PJ first, then retest.
Am I on the right track, or am I still growing dumber?
Yes. When I jet I start with a hot motor and I start with the idle circuit, but only after I'm sure the float is set properly. From pilot to mid to main in that order. I haven't had to do plug chops in about 8yrs but when I did I started with about 20 new plugs and I started with 1/8 throttle increments marked out on the throttle assembly. Now I break into quarters since I won't be doing any nationals or serious racing anymore.