With some measure of qualification being necessary for any challenge to a specious claim I submit this:
I suspect your "intake" is really just an aftermarket air filter assembly and not a complete replacement of the portion of the intake forward of the inlet to the compressor to the turbo. This is significant because most air filter assemblies make use of the stock filter minder (air restriction indicator - a rudimentary yet critical AND functional gauge) and either the Mass Air Flow (MAF) or Intake Air Temperature (IAT) sensor (one or the other not both are present). These two devices (filter minder and MAF/IAT) are upstream from the EGR valve (I am assuming you had an EGR flow related diagnostic trouble code set) BUT they are not directly upstream. Airflow from the turbo first circulates a complete pass through the intake manifold, through the combustion chamber and then into the exhaust BEFORE it enters the EGR cooler and only then into the EGR valve where the sensor for EGR flow could be triggered.
The filter minder's condition demonstrates exculpatory evidence of restriction...simply put if the gauge is set there is restriction, if it is not set it PROVES there is not restriction unless the filter minder is not fully functional. You can run the engine and point to the filter minder as a demonstration of adequate air flow. If this is not sufficient, then the OBDII code reader can be used to measure the MAF...it will either be in the proper range of operation or not...if it is within the acceptable band then the aftermarket air filter can't be inducing a fault further downstream...something else is. If there is not a MAF but an IAT then a comparison of ambient to IAT may be considered...this is not as clear unfortunately...an elevated IAT (this is IAT1 by the way) could indicate restriction through the air filter. Don't let the service advisor direct you to compare IAT1 and IAT2 because IAT2 is post-compressor and will be much higher due to compression (of course, because PV=nRT...the Ideal Gas Law).
Refer to the MotorcraftService.com website's OBDII Theory and Operation section for some GREAT documentation. I have attached a link to the 2005 document (my truck is a 2005) and you should look at pages 2 and 3:
The description on page 2 and the diagram on page 3 demonstrate how there are several elements between the air filter and the EGR valve so there can be no conclusive link without some other evidence. Be professional, polite, and prepared but don't let them use smoke and mirrors either.
I hope this helps.
EDIT: It seems pages 7 through 10 provide the complete description of all sensors involved for the specific DTC...unfortunately it doesn't list the ranges for the sensors in most cases - perhaps the replacement of the aftermarket with a stock air filter and re-check would demonstrate a repetition of the EGR fault and that would indicate the filter wasn't the proximate cause fo the fault.