I don't hear you mention anything about pulling the compression release lever. The auto clutch has a one-way pully that when the wheels (and pedals) move forward the clutch is engaged. You can freely move the bike in reverse without pulling in the compression release leaver as the clutch will not be engaged. Most of us start the bike on its stand with the back wheel off the ground. First kick is with the choke on (if it does not start, choke off or it can flood) You hold the compression release lever in and with the left pedal just past the top you push down on the pedal (kick start) and then release the compression release lever and give it some gas with the twist grip.
If you are going to pedal start, you need to have the compression release lever pulled in while pedaling and at reasonable speed, release the compression lever to turn the engine over. Not sure how you "disengage" the auto clutch... it is always engage in forward motion.
Excuse me for the basics here (maybe I missed you mentioning this) and not trying to insult but want to be sure you are using the best technique.