I have a '99 Air with the 290 carb. The boat we originally test drove was a sport(same boat) with a GT-40. When I ordered, I couldn't justify the 3K upgrade to the GT-40 at the time. I was a bit worried about the power thing until I actually got the boat. No worries for me in that area. Although I always love more power, I have yet to lack for power where it counts. Here are the key differences that I noticed:
1.) Overall Torque and pulling power seemed about the same.
2.) GT-40 was slightly more responsive to throttle adjustments
3.) GT-40 starts first time every time, whereas the carb might take a couple of attempts when cold...to be expected with a carb.
4.) GT-40 top end seemed to be about 3 mph faster.
I spoke with the dealer at length about this before making the purchase, and was not disappointed. Having said that, I prefer to have EFI next time simply for ease of starting.