Ok chaps, I've just got out of my buggy. Been riding it for 20 minutes or so. I might have solved the issue, here's the deal:
At lower rpms, with the pedal depressed all the way, the kart does seem to be slower than with the stock muffler. Acceleration is less, and the top speed seems to be lower too.
However, I tried depressing the gas pedal gradually, 1/4 throttle at the beginning, as it gains some speed I go on to 3/4. I leave it there for a few seconds and then I go full throttle. The kart goes to accelerate some more, and top sped is significantly greater than with the stock muffler.
In my opinion the new exhaust changed the characteristics of the engine entirely. Lower acceleration but overall higher top speed.
Might adjust that by adding a bigger rear sprocket, so I get that little bit more off the line.