Ok, so I've got a few ideas, but first the more info we have the better. Are you getting any CELs (Check Engine Lights)...if so, go to Autozone and get them to scan the ECU(they do it for free) and find out which codes you are getting.
2) What exactly makes you think its the EGR...did the inspection guys tell you it was?
3) When you say clipped the egr pipe, do you mean the mechanic split it open and it is leaking...or that he removed it entirely...becuase if he removed it entirely, he would have needed to make 3 blockoff plates. The vacuum lines aren't what recirculate the air back into the intake, there are there because the EGR valve solenoid is controlled by vaccum pressure. Also what year engine did you get, was it fed spec or cali spec, because some fed spec 91-93 motors didn't have EGRs (so I've heard), so perhaps the engine you got didn't come with one at all.
4) You said the car ran rougher. This again sounds like a vacuum leak. Does your idle seem to be a bit erratic? When your engine is on, and you stand where these supposed vacuum lines are supposed to be...do you hear hissing from air escaping?
If you go here:
http://www.stealth316.com/misc/3tim.pdf
(wait for it to load, as it is a huge document that opens in adobe acrobat)
On the bottom on page 55 shows a diagram of the emissions contol system
http://www.stealth316.com/images/vacuumhoses.gif
here are similar vacuum hose diagrams, they are for twin turbo models, but I think the egr part should be the exact same.
http://www.3si.org/forum/attachment....chmentid=45639
And another, 96 TT model, but should be similar. EGR vacuum lines to solenoid are circled in red.
http://www.3si.org/forum/attachment....chmentid=45640
This is same picture as the last one, but shows how the vaccum lines could have been rerouted to avoid EGR solenoid. If this is your problem, (hopefully, as it would be easy to fix) you could just buy vacuum lines and hose clamps at any autostore and run new lines and fix it.
This is a pic of a guy who removed his entire EGR setup...notice the difference.
Lastly, this site has pictures taken with the plenum outside the car with the EGR removed and blockoff plates installed. This will give you a better idea as to where you should be looking for the EGR ports in your plenum.
http://rdmelton.autoeducation.com/ca...urbos.html#egr
So basically, are you:
1) missing the entire EGR system because you got a different engine?
2) missing the entire EGR system, and you either have a huge hole in the back of your plenum, or it has been blocked off?
3) It is there but the pipe is leaking?
4) It is there, but the vacuum hoses aren't connected so it is inoperative?
If you can take pictures that would help a ton as well.