The Mikuni manual states that they use 2 different main jet systems (needle jets (not the needle)). Primary Bleed and Bleed type, the Bleed one is primarily used for 4 strokes. Will they work, yeah. But you may have a hard time getting the transitions jetted correctly depending on your set up and how you ride.
http://www.mikuni.com/fs-manuals.html
Dwld: VM Carb manual, page 3 (3.2)
Not sure about other brands.
