Update -
The only items external to the engine that I hadn't consiously replaced or swapped are the intake manifolds. I did that a few days ago, expecting that either a) there'd be no change, or b) problem would change sides. Instead, the misfire seems to have gone away!
Only thing I can figure is that I replaced the o-rings between carbs and manifolds instead of reusing them. I always suppliment them with a smear of RTV so it never occured to me to replace them. I've only taken short rides since (it's been too HOT), and need to put my ColorTune on it to be sure but it seems to be cured. Will report back after I give her a good test.