Filing the plunger allows it to extend further down the internal resistor when installed against the EGR-Valve plunger, increasing the resistance which lowers the voltage signal going back to the ECA/Computer. You should prove this before you start hacking away at the plunger.
This code usually is set when the voltage at Closed EGR-Valve is to high. But it can also mean that the EGR-Valve is not closing all the way ((which will lean out the Idle and give you a 41 code) and may cause a rough idle)
As Bill states, the newer/aftermarket plungers are sometimes too long.
Measure the EVP resistance installed, across the Signal & Signal-Return wires as a baseline.
I would tap down on the EGR pintle first, then re-install EVP and re-check the resistance.
You can also shim the EVP up a little to test as well.
With an old EGR-Valve & old EVP, I would suspect the Valve first. Take it off, clean it, beat it with a hammer, check to see if it is closing all the way.
Vinny...
"Do All Scheduled Maintenance Prior To Troubleshooting"
"Resolve All Known Issues Prior To Troubleshooting"