[Kruzin]

Per Federal emissions laws, you should not be putting an engine into any vehicle that's older than the vehicle itself. The emissions standards get more stringent every year and by using an older engine you are tampering with the equipment the vehicle is supposed to have (as you noted, the EGR system is different). By putting that engine in that vehicle, you are insuring the vehicle will not be compliant with Federal regulations:

For light-duty vehicles, installation of a light-duty engine into a different light-duty vehicle by any person would be considered tampering unless the resulting vehicle is identical (with regard to all emission related parts, engine design parameters, and engine calibrations) to a certified configuration of the same or newer model year as the vehicle chassis.

Engine Switching Fact Sheet (epa.gov)