I’m not sure about the exhaust, but the tranny should fit. However, the ’00 transmission is probably a 4R70W transmission and the ’94 is probably an AODE transmission. The 4R70W is an upgraded AODE transmission. The 4R70W is an all around better transmission. So if it aint broke, don’t fix it.
Check out this page for more info on the difference between an AODE & 4R70W transmission: http://en.wikipedia.org/wiki/Ford_AOD_transmission#AODE