Check the float height on the carb as it sounds like it is set wrong. Not sure why you have 2 pilot air screws? take them both out and see if the # is the same. The assembler must have put 2 in by accident. I have a 2003 JR 50 and the bike starts right up and runs good. To unrestrict the bike you need to remove the washer that is tack welded into the exhaust pipe header flange. You can also remove the throttle stop and the bike will go much faster. There is no restriction in the airbox. To tune the Air Screw adjustment on the carb turn the air screw all the way in and back it out 1 1/4 turns. Now turn the idle screw until you can get it to idle steady as low as possible without stalling. Now you can turn the air screw a 1/4 either way and fine tune the carb.
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