How are the hydraulics working? Have you checked the engine oil? I would be more inclined to think that something has caused your pump to blow and dump that much fluid into the engine. Maybe a factory quick connect dead headed your pump.
I would also suspect the seal on the pump, I don't know of any way that it could dump in the tranny. Is it by any chance leaking out the fill in the back of the tractor? I would double check the engine oil level, and I would not run the tractor until you find where it's going. In case you don't know the rear pump is the loader and 3pt pump, while the front is the power steering.
Do you have a valve with quick connects at the back of the tractor. If yes, check that the hoses on the valve if they are all connected properly as we've noticed that we were losing our hydraulic oil from that location. We were also losing oil at the FEL control valve area.
I have spoke with a couple of people on the phone with the problem of hyd oil getting in the transmission.
Not what you want to hear….. but if you were to remove the 3 point lift box assy…. flip it over…. there is a inspection cover to gain access inside the box.