I didn't respond to this post because my car doesn't use stock intake manifold gaskets, but I suppose it would work just as well with either the Ford or Felpro gaskets.
I use Permatex copper spray on both sides of the intake to head gaskets and allow to dry until tacky (about 10 min). Felpro gaskets are better than the ones from Ford.
For the front and rear gaskets, I use Permatex black high temp RTV, but the orange Randy mentioned will also work. The rubber Ford gaskets are better than the Felpro cork ones. I always add an extra blob on the corners where the two gaskets meet to get a good seal. Just before installing the gaskets I smear a light coat (finger width) of Permatex T-Stat & Water Pump sealer around the water jackets on both the heads and the intake manifold. This stuff will dry/cure even if there is coolant present and never leaks.
If your in a pinch and don't have gaskets for the front and rear, just use a 3/8" bead of the black RTV.
Torque the manifold down in three steps using the pattern shown in the repair manual. 1st to 10 ft lbs, then to 15 ft lbs, then allow to sit for 10 minutes and do them all again at 15 ft lbs. Only a few of the bolts actually require thread sealer, but my heads are so heavily ported I just put sealer on every bolt so I don't have to worry.
So far using this method, I've never had an intake manifold leak and I've had it off and on at least six times, including yesterday while installing a new cam.
David