5.0L auto to manual conversion

i posted earlier that the o/d in my cougar went out. some buddies and were thinking about puttin in a t-5 out of a mustang in favor of another auto trans that i will possibly cook. i know that the supercoupes cam with a 5 speed so the knockout for the shifter shoud be there? i haven't checked on that yet. anyways the question i have is has anyone done this to a cougar/thunderbird before? and wat kind of problems will i run into? will i be able to use my ecu with a manual trans or will i have to get a manual ecu out of a mustang? i kno that i will prolly have to get a new driveshaft cuz the trans are prolly slightly diffrent in length. any comments/ideas would be greatly appreciated