I am more interested in where the coolant went than the trans oil. They all hold a little bit on the clutch side.
Well I checked coolant level earlier as I was running it, and it looked a tad more full. Maybe because it was running the first time, and not the second? I am able to safely check the coolant after it's been running awhile. I am guessing because of the quality of coolant (evans waterless), new rads that claim 40% more capacity, and the bike is running so rich is doesn't get very hot. Just a theory.
If the coolant is not in the oil than its fine. Did you loose it or just not check it after the initial start up (air bubble). Trans oil is always stuck behind the bulkheads inside the engine. When I do and oil change I always crash the bike to one side and the other to make to oil get over the internal bulkheads and drain. Jetting, I'm not well versed but the guys have you going in the right direction.
Now that I have given it thought, I put in a slightly incorrect amount of oil. I had just finished getting the top end together, and manual stated after engine disassembly, use 0.63/qt (596cc's), otherwise use 0.58/qt (549cc's). I wasn't using my brain and now realize the manual was probably referring to bottom end disassembly which was not performed. Do you think this extra 47cc's of oil I put in was simply expelled through an overflow hose, or is this difference too small to matter entirely?
How hard are you running this bike? Power valves not fully opening could cause some hesitation. I still don't hear any complaints on excessive or bad smelling exhaust fumes/smoke. I would tap this thing out 1st 2nd and 3rd gear a couple times and see what happens. Maybe posting a vid of how she runs would help.
I have had no problems giving it WOT over and over, I have been running it hard since
Run it and run it hard. It may just need a good clean out after all the assembly live and stuff.
One in awhile I can wheelie with it, but mostly not due to tons of hesitation. I peg the throttle often. It was smoking ALOT before I recently backed off the screw to 2.5 turns out. Many report best success with 1.5 turns out from what I've read. As far as smell I can't help there, I can hardly smell a thing :/ Smoke is white and seems like more an appropriate amount after going to 2.5 turns out, from two.