tool_king, do you have an actual hydraulic shematic of the pilot circuit?
revbill, The info last posted by tool_king does verify that it has a pilot gear pump which means somewhere there should be a relief valve. It could possibly be in the housing you have replaced, if that is the case you will have a (3rd) return line that goes back the the hyd tank or a return manifold. If the filter housing only has 2 lines, one in, one out, then there is not a system relief in it, only a bypass. It sounds like the pump is deadheaded somehwere down the line, and the pump may be only be designed for low pressure. Your description of the internals of the grenaded pump seems to confrim this.
As long as the tank is clean, and your suction hose is clean, you should not have debris entering your pump. I would assume that your system uses hyd return filters, as any good hydraulic system should. Some systems even use a suction screen on each suction lines inside the tank. Since you have inspected the system, I would venture to guess, it is not debris causing the issue.
If you are confident there is not debris entering your pump, you can run a hose from the outlet- pressure side of the pump direct to the tank, plug the hose you removed to prevent backpressure leakage and start the machine. All should be good. If you have access to a flow meter with a pressure gauge and restrictor installed, you can restrict the pressure to the JD pilot spec just for the sake of checking the pump. While not necessary, either of these procedures will verify your issue is on the pressure side of the circuit. Next, you need to determine, without doubt, where your system relief is. Have a pressure gauge "T"ed in the line out of the pump. Normally, system reliefs are either adjustable or non adjustable cartridges in a block, but I suppose it could very well be a piloted spool valve using a shimmed spring. Regardless, before starting the machine, make sure either the relief is backed all the way out, or all of the shims are removed, and if it is a piloted spool valve, make sure the spool moves FREELY and is not stuck. If you have a cartirdge style relief, pull the cartridge and check for debris in the end of it and make sure the spool moves (you could just replace it if there is any doubt), all it takes is a small piece of rubber from a hose or oring to block it. Also make sure the return line from the relief to tank or return manifold is clear. Remove the pilot pressure line (out) and install a hose directly back to the tank AFTER the relief valve, then start the machine. If everything is working properly, you can now set the relief to the JD specs, which should only be around 200-400 psi as others have mentioned here. At this point you can reattach the pilot pressure hose and should be fine as the relief will be doing its job.
Just a couple notes, it is unlikely, but possible that the inner lining of a hose can seperate and block off flow, I have seen this happen with a hose that was pinched, but looked ok on the outside. If in doubt, replace the hose, and make sure you blow out all hoses before installing them. Rubber particles will wreak havoc in a hydraulic system. It is particularly critical to make sure the spool in the relief valve, whichever type you have will move freely. If you cant tell, then replace the valve. Always back off any adjustable type relief before starting the machine, then slowly adjust it up to spec with a reliable gauge in the system.
I tried to find hyd shematic online but was unable. If tk can provide that, we can better determine exactly what type relief it has. Also a parts illustration will show what it looks like.