Starting/running...help.

My bike starts much better when its cooler. When its really hot and 85+ degrees out, it simply wont start without a little throttle.

It seems to run ok, but there is a flubbery flat spot between 2500 and 3500 rpm, then it takes off, but flattens out again across 4500 - 6500, then it takes off again.

I've cleaned the carbs thoroughly several times, used small wires/seaoam/carb cleaner. Set fuel levels while on bike. Manometer synced (which made cruising nice and smooth). Set the pilot air screws at default 1 1/4 turns out from lightly seated. Then tried to "tune" the screws which neither myself or my buddy can hear any change unless they're all the way in or more than 3 turns out.

Stock air box. 4-1 custom straight pipe. (causing flat spots?)