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There is a gear driven round metal rotary valve that sits right behind the carb manifold cover..

Remove the carbs and round manifold cover - inspect for damage

You have already replaced the whole charging system..

Do a battery voltage test while running your engine at 3500 rpm - the battery voltage should be around 13.5 volts..

Do a resistance test...

no - the tests are non running.. You are going to do a resistance test for both tests - the test to ground you want - no reading , no countinunty to ground, thus showing an open

there is a spring chart that lists the pop-off pressure for different spring and N/S sizes - this will get you near the ballpark of spec..
The size is of the needle seat is stamped on it..

pulling the choke richens the mixture and it also increases the carb vacuum - you need to check your pop-off pressure, your jetting, screw settings and check your fuel filters again.

Most Mikuni...

black to black/yellow - magnet "on" switch

black to white/gray - DESS chip reader

can you provide a little more insite into your problem??

to test the stator - unplug the yellow wires going to the rectifier - test for countinuity to engine ground on the engine side of the wiring - should show an open circuit or not grounded..
Now test...