I agree running a coil on 12 volts might wear points faster, but at this point, you need to find the problem. Get maximum spark, if it runs better continue down that road, if it doesn't make any difference unhook the bypass and keep looking. Sometimes you need to sacrifice parts to get a final result.

From what I have read so far,

three different carbs have been on,
timing checked numerous times,
intake not sealed to exhaust,
ignition bypassed,
valves adjusted a few times,
fuel feed from overhead can,

engines runs on its own @ 2000rpm
engine only idles with choke plate closed
engine idles and runs with 16" vacuum
no change when spraying around intake, at what rpm was this done? and what was used?

What is the condition of the engine, rebuilt, refreshed, original running, original unstuck and running? How long has been running?

What is the condition of the intake to head surface? Does it have sealing/locating rings in place? what about the gasket, new, used, sealer?
What about carb to intake, hows it sealed?

When adjusting the valves, are all the adjusting screws even? or, is one or two set different then the others?

Add to the list if I missed something, I am trying to get all the facts for anyone that might of missed something.

What is the weather conditions where you are at? could the carb be icing up at idle since you no longer have heat to the intake? It can happen real easy if the temp and humidity are just right. Try adding a hose to the carb inlet wrapped around the exhaust pipe so it heats the air going in.

Joe