Hello Christopher,
Same bike here, nice ride...
Been a bit, but I think I just cycled the ignition with a hose on bleeder in a cup to cycle fluid through. Every ignition cycle activates the master cylinder when in gear as the AE releases the clutch when you turn the key so you can start. I may have also removed the slave and pressed in the puck a few times as well. Just be careful you don't have the puck (slave piston) pop out or have the reservoir run out. Somewhere someone posted a handy procedure that I followed.
Probably bleed before messing with gear position pot or reprogramming in my opinion
You should also check how much friction the clutch has to final drive while released. That will tell you if fully released. Think I had in in 1st on center stand holding rear wheel. Just don't spin fast or you will get a ABS light/code.
Are you using the proper oil for wet clutch ie. MC oil and no fancy additives?
Ohh, another thing is that a recall was done about gear change motor mount. You may want to check if the superseeded bracket is installed and also check if rod is adjusted properly.
Enjoy!