The only commonality between the 3ph and the HST is the fluid. They both suck fluid from the HST sump, and both dump fluid back in, but that is where it ends.
The 3PH is a red herring in all this because the HST is powered by it's own pump. Going back to the original post, no or very low power but loud whines, Correct? Did it whine as you pressed the go, or was the whine constant?
Have you jacked up the rear, locked a wheel and tried moving the wheel by hand? Maybe there is binding in the gear train, maybe whatever is causing your 3PH valve to crack is also causing this issue. Does the engine bog when you press go immediately or not at all?
I pulled up the shop manual. So based on the diagram of the HST pump, there are two circuits in it. When in neutral, the motor that connects to the HST is not being fed fluid. When in forward or reverse it is, so if there was binding at the HST input from the motor, it would hit the relief valves immediately. Since it is not, and you hear the reliefs engage when you press to move, then it sounds like there is binding happening in the gear case itself.
The PTO is directly connected to the engine via a hydraulic/electric clutch, and not part of the hydraulic circuit, powered via a connection between the engine and pump motor assembly. The engine output is connected to the pump via a shaft, no clutches used anymore.
The 3PH and FEL along with any PBY is powered by an auxiliary pump attached to the engine, specifically, it is attached to the fuel camshaft. So for a few pages, there was unneeded back and forth over something totally unrelated.
So what the OP needs to do is get it in the shop, raise both rear wheels, and go from there. More than likely the problem is in the gear case or differential. Might have a shattered gear that let loose when moving those trees, could have been fractured when it rolled over and just gave up the ghost when you put the tractor to it's limits and a piece is wedged in somewhere.
On your 3PH, once you get the HST problem solved, maybe we can address that one in a separate thread.