I can answer that one!
I have had a Two Bros on my 2004 since new. My idle has always been rough. I also noticed a good amount of exhaust soot on the rear license plate.
One person on Vic's old site and my service manager told me that the ECU couldn't compensate for the lack of backpressure and caused the bike to run rich. The richness causes the rough idle.
It took me 15,000 miles to find a solution. I put in the Ztechnik chip. If you read the info on the chip, they claim that it "corrects the air/fuel mixture due to the lack of backpressure in the exhaust". I now have 18,000 miles on the bike and all I can say is that it RUNS MINT.
They say it is only for the Ztechnik exhaust but trust me it works great with the Two Bros. No more rough idle , no more soot on the license plate and a good strong powerband. Works great!
If you go for the chip be careful that it will work on your bike. I believe 2001 and up is safe. In 1999 and 2000 there are some gray area bikes and you'll need to verify your ECU part number.
Ztechnk and Pirates Lair sells them. I've also seen them on EBay for about $100. The EBay ones may be copies but who cares as long as they work.