Tom,
Sounds like you have reins managing A/F. The two plug colors can come from combinations of things. Since you have two potentially different pistons that may affect the actual compression ratio opposed to matched pistons this is one of the mentioned combination. No air box has an affect from where each carburetor draws in its air, one air source can be cooler than the other. Imagine air pulled closer from the exhaust pipe is hotter, hotter=less dense and therefore your jetting is rich for that carburetor. Oh the list goes on but you can chase that demon.
Jet your carburetors correctly in accord to this choice, one piston wash, two plug color and three plug burn. When you have no idea where to start with jetting adjustment, then you get to reverse the order just given.
While dial a jet is a fairly good solution, it is another wrench in the dyer. Another system to keep track of is the cause of the problem. An example is maintaining five sleds, where one has Holtzman tempa flow, then an ataac another dial-a-jet. Race day sleds are treated different, in each of my sleds I have a lexan card with the spread of jetting needed for that sled. Using mikuni templated charting I just put in the correct jetting. ONCE you get the correct A/F ratio and you write down the temperature and the altitude you are at then all the other situations are known. Eazy Peazy. No more power to generate with the correct A/F ratio, no pistons to burn down or rings to seize. Gas and go wear out some parts.