you could have a lean or rich bog. See where your air screws are at, such as 1 turn out or 2 turns out from lightly seated all the way in. Report back with what you find.
If you have no plans to get cylinders port timing changed for extra stroke, then yes run the spacer plate. I have used the spacer plate on 250r with no problems.
man, jetting the tm mikuni will depend on what size tubes you have. Not positive, but I think the Q4 is what you need with 45/47.5 pilot and 310/320/330 main. Jeff at FAST can hook you up.