This sounds stupid cause I should know it but o well.
I think I have my tranny lines backwards so my question is
Which line goes where?
The front out of trans to top of cooler?
94 zj 5.2

 

Yes
Front fitting is output/hot, it goes to the top of the rad
Rear fitting is return/cold.

What are your problems? The flow path is for the most efficient operation, but I dont think it would cause issues unless your operating in hot temps, or towing heavy loads.
Did you remove all the factory cooler lines? If not there is a check valve in the output line by the radiator to ensure the fluid doesnt drain back to into the trans pan. These valves are know to get debris in them or stop up/restrict flow.

 

I have a major leak when I got the jeep the prev owner had cut the lines rite under the starter and put a hose connecting the lines from the cooler to the trans so when I took the old out I unhooked the lines at the hose that's y I was thinking they are backwards. Today I drove it and drove fine but was leaking like crazy it leaked almost 3 qts in 12hrs. I thought it was the dip stick tube but its clean so its coming from the lines

 

they probably used a fuel line or something which wont stand up to the heat and pressure, those will leak almost right away. id say look into replacing the lines or using a new hose and clamps to replace the hose you have on there now. tranny oil cooler line or power steering hose will work too

 

Crawl This- were your lines correct? Did you solve the problem? I am dealing w/ similar issues after attempting a poor mans tranny flush. I attatched the lines back where they were, but not sure if they were correct to begin w/. My lines dont match the replies either. Could someone link or tell me. I cant find anything. Here is my routing on 96 gc 4.0 42re 242 tc w/ factory cooler. The front line goes to the bottom of my radiator. The rear line goes to the bottom of the cooler. The line out of the top of the cooler routes into the top of the radiator. Is this correct? Also the lines are not warm to the touch @ the front near radiator & barely warm @ the rear where they enter the tranny. (maybe just warm from being next to engine & tranny?) Will look for & inspect the check valve mentioned for clogs. If the routing is correct I will check the lines for flow next. I have checked the cooler & it was free-flowing. Any tips, links or help is greatfully appreciated.