97 Bonneville is just like a 97 GT when we are talking NA, which means the 97 is a 4T60E and the 2000 is a 4T65E. The trans won't work for you.
Otherwise, the only thing to consider when going from Bonneville to GP is you might need to swap the side cover in order to bolt up the mount bracket. Most of the covers have the holes in them though.