[gatzb68]

The longer line from the top of the radiator goes to the top connector on the trans and the short line from the lower radiator port goes to the lower connector on the trans or is it another way? Cant find a good diagram anyplace for the stock ones.

 

[Life is a Enigma]

 

[oldeerslayer]

The bottom line is the hot line which sends warm transmission fluid out to the factory trans cooler within the radiator at the lower port.
Once the hot fluid flows into and through the factory cooler, it then exits at the top to the cooler outlet or return line, which is the top line on your 4l60e.