Seems like there is confusion here between the pulse air system and the EGR system.
The pulse air system has pipes running to each cylinder on the exhaust side of the head, the other end to the airbox. The holes in the head can easily be removed and blocked with a 5c piece and a bit of sealant.
The EGR system has one pipe from the exhaust manifold to the intake manifold, with a vacuum operated valve in between. The most common way I have seen that blocked off is crimp and/or weld the pipe where it meets the manifolds and remove everything in between.