I'm late to the party. (I'm guessing my invitation was lost in the mail.
) So, I haven't read the entire thread, just the last couple pages.
You have an earlier style tank and fuel valve. These have a filter screen and a sediment bowl.
You can test the tank/valve assembly separately without fouling newly cleaned carbs.
Put gas in tank, and an exit hose on the petcock to a gas can. Slosh the tank around while the petcock is set to the reserve setting. If you chose a collection gas can that you can see into, you can check it for debris. You can also check the sediment bowl for debris collection there, as well.
You could also peer about inside the tank for anything that isn't gasoline.
An alternative is to go find a large automotive clear case filter fuel for the above test. Put this between the tank valve and your collection tank. You can recycle the gas in this way while flushing the tank. The clear filter should show visually if crud is still coming out of the tank. Don't neglect to operate the fuel valve while flushing, to get particles out of that, as well.
There is no point in connecting your fuel supply to carburetors until you are confident that it will only supply gasoline without any "extras".
Note that the pilot jets only have an orifice diameter about 0.016 of an inch. Smaller particles with flow through. But, larger particles will stuff up the small jets, making head pipes colder. Almost any particle can stop the full closure of the float valves. It's good practice to shut off the tank valve when the engine isn't running.
After you have total and complete confidence that the fuel supply is clean, THEN connect to your cleaned carbs.
If your supply has been contaminated, all orifices and passageways need be checked for clear and proven flow. Pilot/idle/slow system and the accel pump circuits and outlets. You can check all these off the bike.
The number two bowl can be filled separately on the bench, and the pump verified to move fuel in one direction only after it has primed its passageways. Further, the full bowl can be mounted onto the benched carbs and each nozzle in the four carbs can be observed to squirt/spray into the carb throats. If they don't, then nozzle cleaning it required before putting the carbs back on the bike.
Cheers,