Where does the EGR get gasses from with the Mustang intake? Do they go back to the smog ports on the cylinder heads?
I guess what I'm asking is do they get the gasses from the cross over ports, which were blocked on my heads (I ran a bolt up in them) and I do not want that to create a vacuum leak. But I do want the computer to think the EGR valve is there.

 

All factory heads from these trucks are internally manifolded for EGR.. that's the additional hole right in the middle of the head on the intake port surface. The car style intakes like the Typhoon have a passage in the lower on one side that comes up between the runners.. passes into the upper and is ducted towards the throttlebody, that's the small rectangular port below the TB opening on the upper.
Now.. the cool thing is you don't actually need EGR gas flowing in this port to have full EGR functionality, just put the valve and sensor on there and connect it normally and the computer is none the wiser, there is no EGR flow sensor on this vintage system the computer just looks to see that the valve moves when commanded to.

 

Sounds like a nice project !! I had a backfire thru the intake that drove me nuts!! Turned out to be a Roller rocker i adjusted too tight. good luck gettin her back together and running !!

 

That's what I suspected. I just thought the exhaust gasses that flowed through the crossover passage in the heads came from the pipe that bolts to the back of the head that is ultimately connected to the air tube that runs to the cats, which is disconnected on my truck. I was thinking that when the valve opened to draw in exhaust gases it might suck in raw air and possibly create a lean condition. But, we'll plug it up and see how it works out after a brief junkyard trip in search of the explorer throttle cable bracket.

 

EGR and Thermactor(air injection) are two separate systems on these trucks despite the fact they're both connected to the exhaust. And yes you are right a leaking air injection system can create an artificial lean condition which can lead to engine damage, so if the system isn't needed anymore(no cat) it's safer to completely remove it all and plug the ports in the back of the heads, 5/8" x 1" coarse thread bolts with copper washers does the job very well... RTV sealant will just burn off.