What puzzles me most and since months is the fact that a 40PJ was way too rich on three bikes we tried to jet but it obviously works for you guys. We tried that setting at an altitude of 600ft ( between 8 and 19 degrees) and it was too rich and only just better at 8 degrees. So either it has to do with you guys being close to sea level or it has to do with air humidity.
As I got the Keihin got tuned well finally I could close the matter for me personally. But I am still very interested to get the Mikuni right on a mates bike and it seems that KTM has found something or why would they sell a kit wit very small pilot jets? As Pete said, the PJ cant be compensated by using a "fatter" needle. And, just as a side note, the needles in the kit (xx-75) are thicker than those delivered with the bike and therefore leaner.
Though the carburation can be richer as the needle jet (s4) has a bigger inner diameter as far as I know.
I am curious how bikes with the KTM kit will run, time will tell.