it would be bottle necking it. the whole system should be the same diameter or you wont gain the whole benefit of having a bigger MAF. the MAF might be bigger, but it wont matter unless you have the whole intake the same size.
in addition to the homeade CAI being the same size, you should probably go with a 65mm throttle body if you havent.
ya 5.0 mustang magazine had a tb install taht was a 65mm and they said that even though it was a completely stock except for exhaust, engine, they could actually feel a difference wehen driving. So i say go 65mm as i think stock is 55mm not sure though.