I have this exact same problem, and I've been chasing it for over 2 years now. Still have yet to figure it out. I've done everything shy of a total carb rebuild, that may be coming this spring. Converted to COPs, new plugs, played with jetting/needles, got the charging system to work perfect (14.4v), tried swapping MAP sensors. Nothing has fixed it.
Mine is very intermittent. Sometimes the bike will run 100% perfect for weeks at a time, then randomly start acting up. Just a slight(but noticeable) misfire under steady throttle at highway speeds. It doesn't respond to small throttle changes, you've gotta really juice on it, at which point it takes off strong and crisp. Then it'll randomly stop again. The randomness of it makes me think it's electrical, but when it's "acting up" I can manipulate the problem with throttle position, which makes me think it's fuel. I don't know. It's not a huge problem, I've kind of just gotten used to it. But still annoying. Like how my damn blinkers get all wacky and flash weird when idling, since the bike loses 4 volts between the battery and blinker relay. **** yamaha wiring. I can't just run another line, since then power backfeeds and the the lights would be on all the time even when the key is off.
Be very wary of dealership carb work. More often than not Vmaxers who bring their bikes to yamaha shops for carb work end up taking them to someone else to get fixed again. If you can remove the carbs yourself(which is not that difficult, they all come off as one rack), send them to Dannymax or Sean and they will rebuild them for you, at a cost much lower than a dealer will charge and you'll be sure they're done right. Then just slap the rack back on your bike and go. You can remove the carb rack in around 5 minutes. Remove airbox lid and scoops, remove airbox(4 clamps), remove carbs(4 clamps), disconnect throttle cables, pull off fuel line, done.
As for the COPs, any coil from any modern sportbike will work. The two wires that go to the stock coil packs just plug into the two tiny spade terminals on the COP(they're wired and work the same way). There is a big COP thread somewhere, think it's a sticky. It has all the info you need.
I would try to get a set of COP's with the donor bike's sub-harness so you can steal the connectors. It's possible to get some female mini-spade and slip in there, but I'd rather have the original waterproof connectors. Also, the connectors are pretty universal. I run harness connectors from a R6 and coil sticks from a GSXR750 and they're identical and fit perfectly. Try to get your sticks from a gixxer, they use Denso sticks. Yamaha's use Mitsubishi, which have been reported to be more problematic.
I originally paid $30 shipped for a set of 4 sticks from a R6, and the sub-harness. I then switched to Densos, and paid $20 for the set of four. Yes, they're like $100/ea from a dealer, and no, that doesn't mean $50/ea from some salvage yard is a good deal. Poke around, there's tons of listings on ebay for coil sticks. Just search "gsxr coils" and you'll have a plethora to choose from. Find the best deal and go for it.