I have a JD 490E which was hydraulic system overheating. I started like you with the radiator and thermostat, resealed around the radiators, etc. That was 6 months ago, many thousands of dollars in parts later, with two field service calls by JD techs and the problem persisted. I used a IR heat gun to determine the overheating was caused by the hydraulic system. After a 6 month long chase, the problem turned out to be caused by low pilot pressure. Somehow the low pilot pressure caused the main pump to increase flow, above what the system needed, and the excess flow blew through the relief valves, creating heat. Start with the main pump solenoid valves, check the coil resistance per the test and operations manual. Then disassemble the solenoids to be sure a spring has not broken and wiring is intact. If there are no issues found there, check the PVC for codes. If none are found, check the main system relief valve pressure settings, then the pilot control regulating valve and control valves against pressure specifications.
Please be very careful running the machine at high temps. It appears the hydraulic heat in mine over time has caused all the pilot system valve springs to weaken and at about $700 each from JD, it is going to cost a wad to fix it completely. Replacing the pilot regulating and control valves fixed my heat problem. Now I am dealing with pilot control solenoid circuit pressure issues.
Along the way, the main pump was removed, disassembled, inspected and reassembled. No issue found there. The Tech said the problem was the engine injector pump, (I did not believe him, but he said he had seen it before) so I removed it and had it overhauled (No Change). Then I was told it was the PVC, so I bought a new one and installed it, (again no change). The op and test manual said if the machine shuttered in swing at power level "L", the swing brake was not releasing, so off came the swing motor and it was disassembled, inspected and resealed, (no change). The oil cooler control valves were removed individually, the machine run without them (no change). Others on this site said to reseal the pilot control system which was also done (again no change). We leak tested the swing motor (met specs), looking for a leak by under pressure situation. The main system pressures were adjusted to specifications( no change). Main pressure relief and surge reliefs were set to specified pressure (no change). The angle sensor, P sensor and DP sensors were replaced (no change). It was not until I found the low pressures on the pilot regulator and control valves and replaced them to specifications that my heat problem went away. The heat was created by the main pump being told to increase flow when the flow was not needed. The multiple reliefs simply passed the pressure to prevent system overload, creating heat. The heat source was spread out over all the relief valves in the system, making it impossible to define an exact heat source.