I went back and read your first post, and must apologize for not getting it right to start with. You stated things worked right for twenty hours, not twenty years. My mistake.
Okay, thank you for the valve/lines update. A loader valve with only two lines, mounted between the pump and lift system has been a pet peeve of mine for years, simply because (in my opinion) it's the wrong thing to do. That being said, it's not your problem today.
So let's go back to part where lowering the loader affects the three point. With only two lines on the loader valve return oil from the loader cylinders has no direct path to sump as it does in the traditional three line "power beyond" configuration most loader valves use. Instead, the oil coming back from the cylinders is forced into the line leading to the three point. That oil could be what's causing the lift arms to raise faster while the loader is being lowered. This makes me wonder why the pump may not be supplying enough flow, and the problem may not be in the three point at all.
The 5240 pump has a single suction with two outlets. One for steering, one for hydraulics. Usually if the pump is sucking air, or has restricted intake, it will affect both pump sections and both systems.
You had the tractor pretty well scattered getting the hydrostat out and back in, so you're familiar with most of those lines, seals, and o rings. You would know if any were suspect that weren't replaced during all that.
Yet you seem to feel the steering and loader are working as they should, right? The problem is just with the lift arms? I think what I would try next is a simple air check. Lower the lift arms all the way down. With the engine off, move the lift controls to full raise. Remove the line from the exhaust/return port on the loader valve. Remove the transmission filler plug and then apply air pressure to the line sending oil flow the lift system. If the internal valve mechanisms are working the lift arms (with no weight on them) will pop up. On the other hand, if the system is bleeding off internally for whatever reason, the arms may make an attempt to raise then you may hear air rushing out the filler opening. If that's the case you can't blame the pump.