Many comments and questions in no order:
50/50 Water : MeOH is of course a worst case scenario for high pressure as that mixture yields the highest back pressure under normal conditions. Have you tried flushing the system with pure water and also pure IPA (at low flow rates)?
A black PTFE frit indicates a lot of general abuse and probably no maintenance. Was this a auction purchased system?
Did you clean out the LP Teflon solvent lines, install new solvent pickup filters, insure the mobile phase bottles were clean?
Did you use factory Agilent piston seals and pistons (We know of a NJ service company that uses aftermarket parts and the systems often leak afterwards)?
Did you flush out the pump head with solvent before installing the new parts? Did you flush out the prime purge valve with solvent before installed the new PTFE frit? Did you purge the system with IPA (or pure water, depending on which pressure test method was chosen), plug the prime purge valve with a blanking nut and then run a formal pressure test? If so, what were the results? *That test rules out the other components.
In the meantime, do not connect the system to any columns. Route it to a waste until you can show the pump is clean and runs reliably, then connect a calibrated restriction cap to it and check again, under high pressure (NO COLUMN). "Isolate and test".