The pans are not exactly the same, but they do fit interchangeably. You will need a sidewinder for the pan to fit I believe. There is not enough clearance at the front for a conventional exhaust. As far as I know, the only difference is an exhaust mount or body mount or something on the Gen2.
I have quite a few changes in the works....cut rails, prostreet tank, turbo upperoffset triples, gen2 ECU swap and custom wiring harness.. looking for low-mid 500's for power. If all of those changes don't get me into the 7's, I give up. I think the only thing left of your old bike will be the frame, front fairing stay, cases, Input shaft on the trans, Side fairings, Stator cover, Headlight, throttle bodies, Starter, Rt side throttle tube and controls. I believe everything else will have been changed. Won't even have the same valve cover!