I made a small discovery with the CO mode setting and the FMF programmer. Before I had the programmer on I moved the CO mode from 0 to 10 to smooth out off throttle deceleration. It seems like moving that setting up is like turning an idler screw up, it just makes the minimum amount of fuel flow higher. When I added the programmer set to 3,3,.5,8,4,4 it would stumble when shifting especially when cold. There is a known bug in that programmer where it adds too much fuel when the 5th setting is lower than 6. It didn't seem as good when hot, but 3,3,.5,8,6,4 did get rid of the stumble and that's where it's been all year. I decided this week I wanted to go back a twitcher off throttle so I set the CO mode back down to 0 and on a hunch put the 5th setting back to 4 and there is still no stumble. Bike rides better than ever.
Executive summary: If you install an fmf programmer and you have turned up your CO mode, don't forget to set it back to stock.