well egr stands for exhaust gas recirculation, although now on modern day vehicles with direct injection you will find they dont really use EGR, but modern diesels use it very efficiently (obviously depending upon manafacturer).
The purpose of it is to take a percentage of burnt fuel (exhaust gases) and pump them back through into the inlet manifold to be burnt again, this reduces poisonous gases flowing out through your exhaust, and in effect reduces damage to the atmosphere ozone layer and all that jazz.
Once you have removed the EGR pipes and unit, You can buy the studs as "blanking plugs" for about a fiver from ford i think, although obviously make sure you give them details that it is a ford mondeo with a 2L engine so they can look the number up for you.
edit-as i dont think they are listed for a 1.6L zetec, could be wrong
here is a small picture i posted a few months ago (a bit crap):
