You can clean the runners and the throttle body without removing the runners from the plenums. Unless a mouse has built a nest of carbon crud in the plenums, I recommend that you just remove the crossover tube and hose away into the plenums.
If you do take it all apart, you will need the complete intake manifold gasket set, the Fel-Pro MS94831 from either RockAuto.com or AutoZone.com for about $45.98. This set includes the two metal intake-to-head gaskets and all of the fiber gaskets to allow reassembly of the intake runners to the plenums. You must leave the hose clamps that hold the runners to the plenums loose after the reassembly to allow the intake to seat on the heads. Once the 12 bolts are torqued to reattach the intake runners to the to the head ports, you can then snug the hose clamps.
Again, the only reason for the complete disassembly of the intake would be for powder coating. It is really not necessary for just cleaning the runners and the throttle body. Use a good plastic bristle brush like a drain cleaner to swab out the interior of the runners. Be prepared for a big mess.
If you don't take the intake apart, all you need are two of the Motorcraft E9DZ-9439-A gaskets from FordPartsNetwork.com or FordPartsOnline.com for about $12.49 each. These really only need to be replaced if the black finish is chipping off the stainless steel of the gaskets, but if you have new ones available when putting it back together, use 'em.
