My trans still ran hot after I installed a cooler too. Turned out my engine was running hotter then it should so the transcooler wasn't able to cool well enough. I had a stuck thermostat, fixed that, still ran hot. I ended up dumping my coolant, and flushing my rad from both ends with a hose. Then I took the fan off and back washed the radiator fins - the water was brown. Then took the plastic cap off the top of the rad and washed behind the A/C condensor and the radiator, more brown water.
Now my Jeep runs cool as ever, can even blast the A/C in hot weather (which will effect your cooling by heating up the condenser in front of the radiator), 2 or 4 High climbing long back road hills, which used to cook my engine temps.
Another thing I found was when I pulled my fender liners, my trans temp went down 5 degrees or so, but my engine temp went up a couple degrees (I monitor both on a Trail Dash). Must just be the way in airflow change. Nothing significant but now my engine sits around 103-104 instead of 100 bang on.
TLDR: Clean the radiator, front, back, inside, really good.