I had the same issues with my '03 for a couple of years...sitting in traffic, it would hit the red line, I'd get nervous, cut it off, pull over...it was very frustrating. I did eventually do a full flush of the system, all new coolant, but still had the same problem.
My husband brought home a pricey temp gauge from work and we let the Busa run for over 30 minutes, watching the gauge go to red, taking temps all over the motor, listening to for the fan to kick in. I was relieved to find that I didn't have any real problems at all and although I don't like seeing the temp gauge get up that high, the motor wasn't overheating and the fan was kicking in and bringing things back down. I let the Busa sit in the heat of summer way longer than I would have at a light and was pleased to see I didn't really have a problem at all. It's hard to hear the fan kicking on when you're all geared up and in traffic, but mine was...I haven't worried about it since. Just an FYI...you should check over and do everything mentioned to be sure your Busa is OK, but if you still find it's doing what mine was doing, let it run and listen for the fan cutting on, etc...
I did upgrade my fan to a Muzzy fan too...good luck!