The bike has an Alpha ignition system installed, so no mechanical points/advance.  Going to try and set idle to baseline and try adjusting again.

Success!  I took idle screw and idle mixture screws all back to zero, then set them to recommended starting points.  (1 1/2 turns in for idle screws, 1 turn out for idle mixture screw)  Which gave me a 3k idle speed, clearly too high.  I then backed the idle screws out evenly bit by bit until I got to ~1200.   Then screwed in the idle mixture screws until stumble, then back out to clean idle.  Adjust idle screws, back to idle mixture screws.  Go for a ride.  Back to shop, hook up manometer and use idles mixture screws to get both cylinders firing evenly.

Just got back from a good 30 minute ride, and she now reliably returns to proper idle.  Thanks for everyone's help!