tuff5liter

I have a hook up at a junkyard, and i was wondering if there was another year mustang or another year ford that has a stronger transmission than my 1991 GT. I can get the transmissions pretty cheap just not real sure what i should look for. Does the 2001+ mustangs come with the 3650? i think that is just a rumor someone was feeding me. Any help would be greatly appreciated.