Its ugly but I don't see that as the cause just yet.
A few things pop out in your last video.
[video=youtube;QWC33aTZLqo]https://www.youtube.com/watch?v=QWC33aTZLqo&feature=youtu.be[/video]
1. It's backfiring out of one carb and not both. That's either lack of fuel or lack of spark on one side or a fouled plug behaves the same.
2. One cylinder is very consistent and contributing all the time without missing a beat !!!
That leads me to believe that the cdi is picking up at least one steady pulse and if its picking one up it should be picking up the next pulse.
3. The throttle position seems to make the other cylinder kick in. At idle the other cylinder kick's in and when you punch it to the point where the main jets kick in the other cylinder starts to contribute although its really rough.
One easy way to find out which cylinder is the problem would be to pull a plug cap while running and see which one does nothing and which one kills the engine.
Now I'm going to throw a guess out there that its your mag side that is the problem and that the crank seal on that side is bad judging by the pictures of that whole area.
(thinking rust behind the flywheel cut the seal)
I mean it feels lean... If it was flooding there would be different symptom's but that backfire sounds like its very lean and not to mention that bogg near the end. Seems like only the idle circuit is working and not the full pilot circuit. Also since you said you bypassed the whole fuel system what about the return line ?
Also pulling the choke fully should kill it. You have to pull it on slowly and it should have a big effect between 1/2 to 3/4 choke. That should bring the bottom end up to being so rich that both cylinders should at least start kicking in together. At least if the other one does, that means your definitly running lean.
Now I'm going to throw a guess out there that its your mag side that is the problem and that the crank seal on that side is bad judging by the pictures of that whole area.
(thinking rust behind the flywheel cut the seal)
This is very true. I would pull the flywheel then the mag cover and check for rusty bearings while I replace the seal and clean up the end of the crank.