If I read your setup & changes...that much bigger ATF cooler is keeping your automatic cooler **AND** if your plumbed it back to OEM...that new ATF cooler is sending *COLDER* ATF into the main radiator.
Meaning it was adding cooling capacity to the main radiator and maybe no more with the bypass. Depends on what that bypass is set for
Ask what the 'after market' radiator is, as the OEM radiator is aluminum
How many row?
Staggered?
Flattened?
How many pass or sections?
How many fins on the internal ATF radiator ?
Finally :
Check if the thermostat in good order ? It might be sticking
How many times has the OATs coolant been flushed ? and assume with OATs coolant, not the good old American Green, right?
Check your fan clutch, they do wear out. Just changed mine and wanted severe duty, but NAPA didn't have one in stock. So it now has a HD duty fan clutch (they both couple at about the same percentage water pump shaft RPMs...diff is in the bearings keeping it from becoming airborne). NEVER install a 'standard' duty fan clutch on that engine