OK, I disassembled the carbs again, and confirmed that all passages and jets are clear. Pretty sure at this point that the carbs are not the problem.
I tested the coil, and found two problems. As I said earlier, someone swapped the electronic ignition over from a later 440, but it appears (based on resistance testing) that they continued using the coil for the original points ignition. The points coil has a primary resistance of 3.2-4.8 ohms, while the EI coil should be 1.8-2.8 ohms. Won't keep it from running, but probably not realizing the full added benefits of then electronic ignition.
The second, and probably what's causing my immediate issue, is that the spark plug cap on the left cylinder (which doesn't want to fire) seems to have an intermittent high resistance... about 2m ohms instead of the 5k ohms it should be. That, combined with having the wrong coil, is probably causing spark to break down in the left cylinder.
Speaking of that... I'm assuming this bike should have 5k resistor caps? That's what's on there now, but the whole bike has been pretty worked over by previous owners, and I don't know what has or hasn't been changed.
Thanks for all the help,
Andy