As far as I know the gen2 throttle bodies do not fit the gen1, at least as a direct bolt on.
The gen2 also has secondary throttle plates that the gen1 does not have. These regulate air flow and are used to make the throttle curve more linear and less agressive(they are tuneable with ecu editor). The plates and shaft they mount to would have to be removed and the holes in the sides of the throttle bodies sealed, in order for them to work on the gen1(assuming they bolted on). Otherwise the secondaries and shaft would just be an obstruction in the throttle bodies. IF you could try to use the secondaries you would need the gen2 ecu to control them. Assuming that happened then you have the problem of different head, cams, valves, bore/stroke, and thus fuel/air between the gen1 and 2
I have never heard that the ecu's are compatible between the gen1 and 2 either. I also think that the ecu plugs are different(they may not be, been along time since I worked on a gen1); however if they do plug in, not all the pin locations will be the same.
Some of the gsxr 600/750/1000 ecu's will plug into other models, but they must be reprogrammed to control the bike they are in.
The only ecu swaps for the busa's I know of is upgrading a 99 to 01 model to an 02-07 ecu, and a few other parts are required.
IF the swap could be done, it would not be cheap or easy, as well as having no real benefits.
Best bet is to swap the whole gen2 engine into the gen1, that's been done by several people.
