Like the title says, my exhaust ports are two different colors and I'd like to know why. One is black, the other is white.

I've tuned my carbs recently (although I may need to make adjustments), I have a Yoshimura muffler, and no petcock - the fuel is connected directly to the carbs (which I'd like it fix with an on/off valve if anyone knows of a good one).

I could be wrong but it seems like you may be running rich on one side and lean on the other.

I think that's the right idea...I'm just not sure how that would be possible. Or what could cause that.

"I've tuned my carbs recently (although I may need to make adjustments)"

Its possible that that adjustment you need to make is too balance them...  so that equal fuel is gettin too both.

Well what do the plugs look like. That is more important than the exhaust ports. But yea they should be close, you can have different float levels, or be sucking a wee bit of air in 1 carb ... so one richer than the other can happen.
Cool.
Buddha.

The plugs look different, but not like they are in bad shape. I can't recall exactly but one had a slight discoloration when I checked (it didn't look extremely abnormal so I put it back). I tried to match the turns for the air exactly. Could one of the carbs be flooding, causing this to happen? Is it a BAD thing to have the exhaust ports two different colors?

I replaced the plugs about 4-5k ago before I tuned the carbs.

Do the cabs synchronization, and the colors will be same on each side. Then this job will be done, second job will be the mixture.
After that all will be ok