I got the bike fully assembled, put in my spark arrestors and went with the stock fuel map, so I can compare to before the work. Its actually running pretty well overall (better than before the work), but I still think the rear cylinder is weak. At idle I'll occasionally hear the rpm blip up and there's kind of a 'chuffing' sound in the left exhaust pipe. Just sounds like it's not hitting right compared to the other side (I'll have to check for exhaust leaks too). I also get a higher RPM vibe through the whole bike.
Good idea about switching the sensors around. I was going to fiddle with the TB balance some more so I'll see if it's possible to switch the sensors w/o removing the tanks