I just rebuilt my motor from oil pan up, and didnt connect the egr back up to the supercharger, I made a block off plate that goes in its place. As for the manifold, I left the big nuts on there and then found a bolt that fits into the nuts, (this way the bolt isnt inside the manifold) and then welded up the bolt and nut.
There is no problems with the car at all, some people say that the check engine light will come on, but it doesnt.