The backfiring was coming out of the exhaust. How would it come from the carbs?
Back fire in exhaust could be a build up of fuel. Carb back fire can be from early ignition timing, lean mixtures, poor valve seat closure etc.
Or, in severe lean cases, no pick up at all. This sounds more like what happens when i hit the gas from idle very quickly
Still sounds like accel pump issues, to me.
I'm guessing you didn't properly clean the two check valves in he accelerator pump circuit. or verify they function properly. I cleaned everything, not sure about how to make sure they were functioning properly though
You can test the pump by pulling off the #2 float bowl with the acel pump attached, filling it with gas and actuating the pump rod. If it's working, you'll need safety glasses for continued good vision.
Did you check the holes in the periphery seal were open? I have no clue how to perform this step
See attached pic. I had to drill mine open again, as they were swelled nearly shut. Be carful not to tear the rubber while drilling, or you'll have a leak.
Did you verify that all the squirters in each carb shot a nice even burst of fuel when the throttle was applied? yes i checked everything by using carb cleaner and shooting some into the holes and got nice pretty mists out the other holes and ends, the jets were clean for sure!
I put the carb bank in a bench vise. Reinstalled the #2 bowl filled with gas, and worked the throttle a few times. You can then see if all nozzles are squirting and with the same intensity.
Electronic tachs (test equipment) can be purchased that use the timing pulses from the ignition to calculate accurate RPM.
Even without the accurate tach you should find the proper IMS setting to correspond to the mods made to your bike. I doesn't seem likely the stock book values will be relevant.