Personally I'd NEVER put anything in the cooling circuit that has the ability to restrict flow (filter/check ball). The heat exchanger has large enough coils where debris isn't a problem, however, the trans cooler at the front should be replaced, especially if you've now experienced repeated failures.

I know it's been suggested a few times, but here it goes again. Find a trans builder with some true talent. I used Dave Goerend for my personal build and bought the converter and valve body kit from him. I've had 90k of NO trans issues since doing this. I've also had several customers that had trans troubles (most of them pulling stupid heavy out here in the heat) and they pulled the trigger and bought complete units from Dave and I did the install. Five of these are local and the trucks have been running flawlessly for years.