yes there is a HUGE difference. the reason i went with the same mm carb is, i have alot of friends who race and i also used to race so they shoot me straight, anyhow. 39, 40, 41 mm will give you a crap load of top end performance., you get the same performance as those carbs with the 36mm just not on top, i ride the dunes so i wanted STRONG mids, thats this carb it has a flatslide in it and the ventury tube is set for racing. also it has a adjustable pump which lets you set the fuel where you want it, right now i have it set to run on the main jet till just past 1/8 throttle, then from ther e to just past 3/4 throttle it runs from the jet as well as the straight stream of gas being shot right into the motor via the pump and at the very top the pump is off and it runs on the jet again cuz you don't need it at full throttle.
the company claims 6 1/4 HP gain bolt on with a K & N, i believe them cuz my z hits like a 2 stroke, when that pump kick in it is like mega fuel making mega power, thats why i am getting stage 2 hot cams to increase it even more and the 440 kit will be a great accent to what i have aleady done. plus i am selling my yoshi slip-on and going to get a CT racing pipe should be right around 47 HP or so and mids that will throw sand from here to space.
so to answer your question yes, you can get a huge gain with a mikuni race carb check out
www.sudco.com go to the tm flat side race series and read about it, this is the same type of carb that is on a GSXR just smaller mm