Clean/replace the needle and the needle seat also.
Clean the PC too(if using the old one).
You can purchase a kit from Agilent that includes the needle, needle seat, plunger seals and I believe the rotor seal for doing routine maintenance on the autosamplers.
You will also want to replace the teflon frit in the bypass valve. You can take the plungers out and inspect them under a magnifying glass and look for any scoring, if they are still smooth then you should not need to replace those, just the seals.
Other parts that could have been damaged if sitting dry or with water instead of solvent would be the outlet check valve and the active inlet valve. Do the seals and frit first, then if you have excessive pressure fluctuations start with the outlet check valve. It if builds pressure but doesn't hold it the outlet is most likely the problem, if it just doesn't build pressure then it is the inlet valve.
Also after sitting for so long, make sure to check that the four solenoids on the solvent channels are working correctly. One easy check it to place solvent in bottles on all four channels and run a 25/25/25/25% mixture, few ml/minute for an hour and check that the same amount of solvent was pulled from all the bottles. Actually is it probably easier to place the solvent inlets into four 100ml graduated cylinders, prime all four channels then fill them to the 100ml mark before starting the test, that way you can easily see how much was pulled from each channel. If they are not within a couple ml of each other then you could have something either blocking the line or holding the needle valve open allowing improper proportioning.
