The gearbox differences are most likely due to mileage, the Rotax is a clunky bitch when new, but gets better with a few miles - assuming both chains are properly adjusted, if it's too tight it affects the gearbox.
The Tuoldo does feel arse up and tall compared to a Gen 2, regardless of where you have your forks - they are slightly bigger frames etc.
Engine - the Gen 2 is normally smoother than the Gen 1 (running Map 2 on both) the flat spot is 5-6k - your revised chip probably masks this. It is noticeable as a hesitation as you hit the gas from low revs, then you get 6k and the front wheel leaves the floor. After even a few weeks you instinctively ride around it and don't notice it. If Gilo's is lumpy it probably needs setting up properly - go see Griff. It could be TB's etc.
My Tuoldo with an airbox, PCIII and Akra 2+2 system, was pretty much identical in engine characteristics to Liz's Gen 2. My Factory has an airbox and Ape Ti cans and eats either on track. On the road, the differences aren't worth mentioning, it's all at the top end and how often can you really stay on full throttle?
PS - unlike some recent posters I can tell the difference the expensive ***** makes, and arrive at the cafe with my mates for a sarnie - but then again I have some mates.