erm the 998 frames (and 748R) have a different cross member under the airbox (the bit the coils fit onto) to allow the shower injectors and big airbox to fit.
so you can put a 996 lump into a 998 chassis but not the other way round without some mods.
Yep 998 has the same frame as the 748R and 748RS with the different cross member It also uses 2mm larger diameter engine mounting bolts. The coil mounts are also in a different place