Hello,
After a full day of jet swapping and test riding I think I found a good setup for the Mikuni TM40 on an XR650R.
First of all, I'm below 1000ft. altitude(Florida, USA). The motor is stock, headers stock. The pipe is a White Bros. E-series w/ 12 discs. The stock intake manifold and airbox has been fully unrestricted and a UNI aifilter (no holes in side covers, yet).
I tried pilot jets from 22.5 through 27.5 and test rode each. I ended up sticking with the 25 pilot (pilot screw 2.25 turns out). The bike starts first/second kick with no choke, response is crisp and strong. Popping/overrun when closing the throttle is at a minimum but is still there (22.5 pilot had almost no popping, but didn't feel as stong as the 25).
The 9DJY4 needle worked great in the middle postion so I didn't mess with it. No surging while cruising (like stock carb), and accelerates clean and strong from 1/4-1/2 throttle on up.
I was unable to get full throttle very much, so the main jet is still questionable. 3banana recommended that a 140 was a tad lean, while a 150 was perfect (dyno'd with aftermarket headers). However, I tried a 142.5 and 145 and left the 145 in. With stock headers, I figure definitely leaner than 3banana's 150 main jet. So a 145 main 'seems' about right. Acceleration was clean and strong during short periods of full throttle. Extended full throttle might show something different though.
I'm quite pleased with the carb to say the least. It really wakes the 650R up. The whole powerband is strong and smooth with no noticeable holes or hiccups (butt dyno

). I still plan to experiment when the accel pump kicks in, right now it comes on at ~1/8-1/4 throttle on through 3/4 throttle.
Just my findings. Still open to other suggestions... Thanks.