The Mustang Cobra R comes with a 5.4L engine and a tremec transmission (i think this transmission) and it has a different hood for clearance. I also ran across an article awhile back about a guy who took the V10 6.8L engine out of a wrecked Econoline van as well as the trans and got it to work in his ex-V6 mustang and he said that it had tons of torque, went like crazy and was reliable as well as not that expensive to swap over.
actually here is the address:
http://www.gulftel.com/vnomsss/topnews/mikearnett.htm
I'll actually post this as a new topic as well so other people who might not believe this can see.