Your manual tranny does not need a cooler and therefore has no cooler lines. Da Zone gave you a radiator for an automatic and probably that is all they stock. If you are adventurous, plumb the tranny cooler to your engine as an oil cooler. Otherwise, cap them, or not, and don't let it bother you.

Hey, what part of the Poconos are you in? I was born and raised west of Wilkes-Barre (West Wyoming). My dad used to race at the old Pocono Drag Lodge in Bear Creek

Here is a video, I am the fat blond kid at the end. Now I am a fat gray old man. LOL

http://www.youtube.com/watch?v=tQKp3QR5Los