Yes, of course it'll run. The main jet will make no difference to the way the pilot jet works or the cutaway or the needle until the area around the needle as it's withdrawn from its jet is greater than the area of the hole in the main jet.
Look, there's a system for setting up carbs. It a logical evidence based approach that will work if you follow it. Being convinced that you know best and just shoving new bits in at random really is an amateurish way of trying to solve problems. Dismissing checking things because the bits are new is just stupid. Set the carb up from scratch (half of it sounds as though it's not far out anyway) and check the advance is not only advancing but that the curve is what it should be. It's not hard to do and as your engine is not a std setup it's the only way.