The pilot screw on these carbs is an air screw. It mixes air with the pilot fuel. The fuel is controled by the pilot jet in the bowl. ALL the passages for the air and fuel MUST be clean in order for the pilot circut to work properly. Air box mods and/or removal will have a great effect on it's operation.
Double check your cleaning of ALL the carb the passages, get the air box on right and used the factory setting for the pilot jet and screw. It should be very close with only a minor tweaking of the pilot screw (1/2 turn either way at most).
Good Luck,
Phil (opsled)