I like the real Mikuni/Yamaha stuff and usually buy individual parts when I can. However, I have tried some of the Japanese aftermarket stuff and have had good luck with the kits made by Keyster (unfortunate name, but good quality stuff). The stuff sourced from Taiwan looks suspect to me, especially the ones that include jets and needles - run from those. If you have the genuine Mikuni jets and needles, they will clean up just fine.
Depending on what you want to replace, the following Keyster kits might do the trick:
K-0324
K-1492
K-1494
I personally used the MikesXS basic kit #48-1408 (which looks to be made by Keyster). Then I bought the balance from Yamaha (butterfly shaft seals, pilot mix screw o-rings, bowl drain o-rings and float valve filter net). When I looked at it, this was least expensive way to do it for me.