Which line is which comming out of the trans? Also what size are the fittings and what size line/hose should i run to and from the cooler?

if you're gonna run an auxillary cooler and the cooler in the rad, then make sure you run the fluid thru the rad first and then the auxillary cooler. this will give you optimum cooling.
also, make sure you use hose/line rated for ATF. fulel line WILL NOT work for long. the fittings on the case are standard thread and take 5/16 hard line. you should also try to run as much hard line as possible. much less chance for leakage that way. make sure the ends of the hard line are flared if you're gonna put soft line on them, or they will slip off in time.

Take one of the lines off the rad and fire up the engine. The fluid will either come out of the line or the radiator. Then you will know for sure. Might want to put a rag over the ends so it doesn't shoot all over the place. :D