That's great Atlas,
I'm glad you followed-through on the vintage Honda 350 twin rather than 'just enough to get it running and out the door' as I've seen So many PO's do to 350 twins;nice work.I imagine you might have had the choke in the wrong position for running when warmed up causing your rich running problem? just a guess,it happens.
Winner, winner, winner! So embarrassing..but even reading and trying to understand I just couldn't wrap my head around it. The only way I was able to "get it" and finish up the bike was to read along that chapter in the manual with the air box removed to visualize the choke action. With the choke in the "Open" position, the choke valve is OPEN, this is the natural run state for the bike. With the engine NOT being choked for air.
With the choke in the CLOSED position, the choke valve is CLOSED and the engine is getting restricted air. This leads to a richer fuel mixture, good for first starting the bike (but not for prolonged running!!).
Anyways...with a better understanding of that system we were able to confirm that the biggest issue with the bike was indeed the human behind the wrench.
But I am happy to report that with this newfound knowledge we we're able to tune the bike sans-problem. She is running like a rocket! The fixes we did were all in benefit of the final product. The new ignition will allow the owner more freedom from maintenance (and the old points were shot), the spark plug caps were at their resistance limit, the carbs had mismatched jets and one was completely locked with varnish-like fuel. The quick disconnect is a nice improvement (and yes 540nova slightly longer lines would've been a better idea!), as is the battery tender. The new tires are totally awesome!! We definitely took the long way around but I think the new owner is going to be really, really happy when he gets this ol girl back. She feels like a totally new bike.
PS I think the root of the choke confusion comes from A) a previous lack of complete understanding of the system (I though choke increased airflow...d'oh!) and B) the "Enrichener" mechanism on our airheads which is push DOWN to engage, the opposite of this choke system.