I appreciate the feedback as much as I hate to hear it. Originally my plan with this bike was to make it a reliable daily ride, and with that goal I wanted to keep the stock airbox, update the electronics including putting electronic ignition on it, replacing the reg/rec and in general just refine things to make it a solid bike to ride.The Mikunis do seem a lot easier to tune than the stock carbs, but losing the airbox feels like a step in the wrong direction from my ultimate goal.
To answer your questions Teazer: I didn't get any info from the shop on the carbs. Like I said I got in there the day before they left for a winter break and I haven't talked to them about the specifics yet. I believe the carbs are 32s? The inlet side is 57mm (2.25") but I haven't had them off the bike to measure the outlet size. I checked compression before all this and both sides were good (I don't remember the numbers, a friend helped me with that). The timing has been checked by multiple people and I am pretty sure it is set up correctly.
The big question you ask is do I know that everything else is perfect?
The answer is an emphatic no. That is why I took it to a shop. I hear you pidjones, and I too am here to learn. This bike has proven to be a larger learning experience than I expected and I am grateful for the help of others that have helped me make progress in this training academy.
After the short ride the other day I pulled the plugs and it looks like it's running rich. The left side is richer than the right. The bike starts fine and once it gets up in the upper RPM range it seems like it wants to go, but the low and midrange are really bad, so I decided to move the needle up. It was in the middle clip position and I raised it one. It is still lagging, but it does seem to have improved things. When I was letting it warm up, I could hear and feel that the left exhaust was more sporadic than the right side. On the right I could feel consistent pulses of exhaust, but on the left side it was not as smooth feeling.
As far as going back to the stock carbs, I have all the stuff to do that, but with the Kehlins I was stuck in a dead-end with a bike that wouldn't run, and now at least it moves and has given me some hope that it will be able to improve to a useable state with some additional tuning. I'm willing to keep the Mikunis.