yea, using the GT-40 heads would solve the issue. or, like i said, you could get a chip programmed with an EGR delete. you could run it as is, but it would throw a check engine light. no big deal, as a strip of electrical tape over the light would solve this.
and yes, there is more to it than plug angle. basically, from what i understand, the 96 computer controls EGR function in a different way than the 97-up. dont take my word as final, and i suggest you get a 2nd opinion.
there are many, many stangs out there with headswaps and no EGR. i have seen a few threads on the stang corral were a couple of guys in Cali. were running no EGR and still passed smog. like i said, it is not the be all/end all smog part. it would be better to have it, but you may pass emissions without. best bet would be to seek out a mustanger with GT-40p's and see what they did.
if it were me, i would take my GT-40's, have them "cleaned up" with new springs etc., and slap 'em on the new motor. but, thats just me, and you need to weigh all your options. you could sell your GTp's for about the same $$$ it would take to do a mild rebuild of the GT's. might as well go through them while thier off the motor. this would basically put you back at "new motor" status with little/no extra expense.