If you unhooked the loader, you need to connect the tractor quick connects together so there is flow from the pump back to the 3PH control valve. If you just disconnected the lines, this deadheads the pump and can break the pump(blow seals, crack pump case) if you try to run it this way. Quick connect fittings being inadvertantly opened while the engine is running have been the cause of many pump failures. One suggestion is to place large ty-wraps or zip-ties around the QC body to keep them from accidentally being opened.
I wouldn't think the front end loader valve has anything to do with the 3PH problem as the fluid basically just flows through it unless you are performing some work with the loader. Since the 3PH holds weight with the lowering/speed regulating valve closed, there is most likley nothing wrong with the lift cylinder seals. The valve itself is pretty simple. Fluid enters from the pump(or FEL valve assembly if so equipped) and when in the "neutral" or "lower" position flows right into the resovoir. When you move the control lever to the "Raise position, this flow from the pump is diverted to the 3PH cylinder input, pressure builds and the 3PH raises. When you return the lever to "neutral", the fluid in the cylinder is trapped there. When the lever is shifted to "lower" the fluid in the cylinder is released back to the resovoir along with the flow from the pump and the 3PH lowers. Between the control valve and the cylinder is a pressure reliefe valve and the speed regulating valve. IF the pressure reliefe valve is leaking, the fluid will take that easier path back to the resovoir instead of lifting the 3PH load. This valve is located on the top front of the 3PH loader control valve part #s 1-7 on the linked picture at John's Jinma site.
http://johnstractor.homestead.com/files/HydValve.jpg
As the pic shows, the valve is located under a square headed pipe plug and consists of a spring, some shim washers and a valve that seals a hole. If the pressure below the valve exceeds the spring pressure then the valve opens and dumps fluid back to the resovoir. This valve also helps protect the 3PH from shock loads that occur when bouncing a heavy impliment over rough terrain.
The only filtration is a brass screen strainer located on the suction line inside the resovoir/lift box usually accessed from the top of the resovoir. The 3PH lift cylinder is also inside the resovoir.
With a front end loader there will be 2 safety valves in your system. One is in the loader valve. If you attempt to lift too much weight with the FEL, that safety valve will open and allow the fluid to bypass the overload and continue on to the resovoir via the 3PH control valve. The second safety is in the 3PH loader control as described above. I had a problem with my 3PH safety valve. The safety was set too high. I had the 3PH speed regulating valve closed too tight placing a lot of restriction on the fluid as it entered the 3PH cylinder. Every time I lifted my brushhog, I sent the pressure in the system over 3000 PSI. The first failure I noticed was at the "O" rings on the loader valve. They started dumping fluid on my right foot every time I lifted the brushhog. This excessive pressure was also felt back at the dump trailer quick connect that my 284 came with. It bent the cage assembly that holds the checkball and the QC fitting started to leak whenever I lifted the brushhog.