There is a vacuum diagram that I have that Ford Racing supplied to me when I installed my GT40. If you want to shoot me an email or a PM with your email address, I'll try to scan it in and mail it to you tomorrow. For now, here's what I can remember off the top of my head.
The hole right by the main inlet gets plugged.
On the underside of the manifold at the very back there are two more holes. The one that will sit towards the back when the manifold is installed needs to go the the brake booster I think? Its a pretty good size vacuum hose. The other one gets plugged.
Then there is that little metal bar that runs horizontally across the underside in the middle of the manifold. There are two vacuum ports on the ends of this. On of these you will need a vacuum tree for (The back one I think, not that it matters) The tree will need two small (3/8?) vacuum outlets, I don't remember what these get plugged into. The other one will need a single larger vacuum port, I don't remember what this goes into either, just make sure all your vacuum lines are hooked up.
Once again, shoot me an PM and I'll get you that schematic when I go home tomorrow, or I'll just look at my intake and tell you. The above was done from work, so I'm just going on what I remember. Sorry for the long post, I remember how much of a PIA this was.