The main jet size is for wide open throttle. The pilot jet up-size would have helped your original complaint of hesitation at steady state throttle. I believe what you had was lean surge, and since gaskets fixed your original issue, that was the case, but the jetting would have been a band-aid working around the air leak. If you have to use excess mixture screw, that's still your pilot jet needs to go up. Low speed issues will most always be air leaks, or the pilot jet. Your mid-range roll-on performance is needle height and taper, and the WOT is the main jet. That's just general CV carb stuff, and the circuits overlap. For the final word on any of these carbs in particular, 5twins can get you straight.
Also, you can cause yourself a world of headaches by trying to jet when you are not sure you are airtight on the intake side, and/or when the carbs are not synched up.