Trying to make sense of your latest test...opening up the throttle as you did would certainly bypass the pilot circuit (and any fuel flow problems the pilot circuit may have). You'd be running on the jet needle at that point. Your test suggest you got more fuel into the cylinder. So that's good.
The backfiring isn't good though. Most backfiring can be from raw fuel collecting in the cylinder and exhaust and at some point the whole collection combusts in one big bang or smaller bangs. Problem is, you say there was no fuel entering until you decided to open up the throttle. No fuel could have collected before you opened it up. If that was true, then your needle circuit also has a problem and/or, the spark is intermittent. I say this because your test was while running on the needle circuit.
A weak spark will obviously cause backfiring but so will too much fuel.
I don't have time now but I'll try to think of the problem and come back later if you still need help.
Something's causing poor combustion and it's not compression. So that leaves a weak spark or carb problem. 1 and 4 are fed by one coil, so it suggests the coil isn't the problem (1 is supposedly good), but it's still possible that other conditions/differences exist between cylinders/carbs 1 and 4 that help #1 keep firing, though it may have a weak spark too.
Do you have a manual and multi-meter? Test the coil resistance's and voltage first because it's simple. If it passes test, then you just have to check/clean any plug cap or plug lead problem. That would cover any #4 spark problems. HOWEVER, I'm not that familiar with the ignitor tests on your bike. Seems to me the ignitor can cause a weak spark at two cylinders also. Anyone? Perhaps your manual will help?
Anyway, check the coil, plug connections and possibly the ignitor. Basic maintanance that should be done anyway. If it passes, you KNOW it's carb related and we can focus on that. If you have a meter, the electrical tests are much quicker/easier than tackling the carb.
Hope I'm not making you do any unnecessary work, but backfiring can be either fuel or electrical and we have to eliminate one so we can focus on the other.
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