[dsraven]

the trans bolts with the extra "stud" are for mounting the trans dipstick on the pass side and also the fuel lines on the drivers side of the engine. there may be a few other things that would be application specific as well but that is up to you at the time of install. some guys will use a stud at each location so they have the future opportunity to use the stud if required later for something unforeseen. a vacuum plug over the stud threads will keep it looking good plus keep the firewall from damage upon engine install