My first task would be to learn why #1 shows different spark plug deposits than the others. Vacuum sync would be my first step. Swap the "different" plug for another position, or replace plugs to learn if that gets them all depositing the same patterns. If not, compression test, float height, etc. Did you verify the emulsion tubes were clear and the orings for jets are sealing as new?
The UNI NU-4055 filter works fine. It is NOT going to cause a single cylinder plug deposit difference. However, that and the exhaust change might change the ideal pilot screw setting. Without knowing the exhaust flow difference from stock, I can only guess that turning the air screws inward 1/8 turn might help.
Mark your throttle. In any gear, from idle speed, the engine should accept without stumble up to one half remaining throttle travel and accelerate reliably (even if not particularly briskly). That is how the idle screws are set for this model using no-stock configuration. If the engine stumbles, you need to turn the air screws inward. if you have have trouble with plug soot fouling with prolonged idle, the air screws need to be turned outward.
There is no good reason why the timing for idle and advance positions shouldn't be identical. And, if you wish the idle to be smooth with minimum trans gear clack, it better be identical between 1-4 and 2-3 at idle speed.
Without a run time log report, we can't tell if the engine's been sitting for a time. There could be specs of rust inside holding valve a bit open and rings binding the piston grooves, etc. A compression test will give a current engine health overview. If one cylinder has less compression that the other three, you can't expect it to behave like the others and no amount of carb tuning, duct air leak investigation is going to fix the situation. However, another 100 miles of operation may get all the parts happy with each other again.