have a 97 mustang auto trans and itd id the same thing as yours, turned out to be a bad torque convertor, but had to replace alot of internal parts in the transmission due to the fact that little peices of the torque convertor circulated around, as far as your misfire just start off with your basic tune up which is wires and plugs if that hasnt been done recently, real easy to do on a v6 mustang. now the overheating issue i would do a pressure test on the car to make sure there is no leaks, also make sure the fan clutch is working properly, is there any white smoke coming from the exhaust if there is then a possible intake/head gasket problem with the car, and to be honest with you if all this is going on with the stang i think it might be cheaper to get rid of it now.