I have a 4 Cylinder '99 Accord EX that, after it warms up, when you push on the accelerator it will start to move then acts like it wants to stall, then will surge, and then act like it is going to stall again. If you hold steady on the accelerator it will just keep doing that lag/surge behavior. Usually it will take off if you give it more gas, but not always. It will then typically do okay until you stop at which point it will act this way again. Often if you just let off the gas then press on the accelerator it will do this lag/surge again as well. Today I tried pressing on the gas with the car in park and the engine behaved the same way in park as when driving. I have replaced the TPS and checked for vacuum leaks and did not find any. While I had the throttle body off to replace the TPS I cleaned it up pretty good as well. I also pulled the vacuum line off the fuel pressure regulator and there was no gas in the vacuum line. It does show a code for the knock sensor, but that was recently replaced and seems to be working as it should. I have not had this car all that long and before I bought it it had a cracked head repaired. Since I have had it it's also has had the EGR passages cleaned, a new distributor, new plug wires, and the knock sensor replaced, because it would often run rough. It was doing fine for about a month then the lag/surge thing started. it was intermittent at first, but now it's quite constant. Also the lag/surge will vary from fairly subtle to quite aggressive.
I can't imagine it's related, but the power door locks make dull clunk but don't operate either. Other than this drivability issue (and the door locks) the car is in pretty decent shape. I can live without power door locks, but this lag/surge thing is not an issue that can be lived with. Any help as to what may be causing this would be appreciated!

 

Just because the FPR is not leaking fuel does not mean it is functioning properly. If the spring/damper inside the regulator is faulty it may be loosing fuel pressure or rapidly change it.
Actual fuel pressure should be checked.
Did you ever check the MAP sensor is functioning properly?
This will require a vacuum pump and voltmeter to monitor change. Vacuum and voltage should both change linearly, if the voltage spikes/dips during smooth change of the inHg then that may be the issue with the MAP sensor. Back probe the sensor while it is electrically connected to the car.

Always get back to basics as well.
Verify the battery is clean, fully charged, and holds a charge 12.4-12.6 Volts.
Verify the battery terminals/cables are clean and tight.
Verify the ground terminals and all ground leads, connections and jumper/bonding cables are attached, clean and tight. Since the head was removed the wire harness was definitely disturbed. Verify the ground bonding jumper on the engine mount was reinstalled. And the main harness ground is installed as well.
Verify there are no broken or damaged wires in the harness.