I believe he can fit the 999 engine into the 996 frame. Skidlid has done this I believe with his hybrid 998. but has for swopping frames, I can't see the point. The 99 bodywork just won't fit the 996 frame.
I find it stupid too, but a new 999 frame costs a lot and he already has the 996 one... anyway if it doesn't fit ok and it needs cutting and adjusting, i will really advise him not to do it
I'm unfamiliar with the 2002 996 frame, did it have the dropped tube for the larger airbox as per the Foggy rep frame and the 748R frame and the 748RS frame on my 998 Hybid. If not then fitting an air box along with shower injection may prove difficult. Also the Testastretta engine uses 2mm larger diameter engine bolts for mounting in the frame compared to earlier 996's , the 748R and 748RS also use tha larger bolts and these were introduced in 2000 so could possibly also be used on the later 996's
When you say frame swap, I would have thought it would be more of a engine swap, as fitting a 999 bodykit onto a 996 frame will give a few headaches as no doubt will fitting the Radiator, headlight and a few other items.