Actually those block off plates are for the center crossovers. On the intake gaskets there are two holes in the middle of the gaskets that can be blocked off if desired.

To help with water leaks I put a thin bead of RTV around the front and rear coolant passages on the heads between the heads and the gasket. This also helps to hold the gasket in place while you're putting the manifold on.

As far as the end gaskets go I wouldn't use them due to exactly what you're going through right now. Use regular RTV not the "Ultra" stuff that Permatex sells. Spray some brake clean onto a rag and wipe both the end rails on the block and the end rails on the manifold. With the intake gaskets in place run a continuous 3/16 or so bead of RTV from end to end on the rails. Then being careful lower the intake manifold onto the block keeping it level and centered. Then torque as specified.

 

In place of gasket sealer, you can also use 100 percent silicone window caulk. As far as the block off tabs on the intake crossovers, I think they are to remain open for intakes with the little springy heat risers that open the choke,,,with the crossovers open the intake warms quicker opening the choke sooner.

 

If you do want to use the rubber end seals, you might try drilling a series of shallow 1/8" holes in the block rails. The holes tend to bite into the rubber, keeping it from slipping out quite so easily. Old Chevys had deeper holes in the rails and the rubber seals had spikes that fit into the holes, and they stayed put just fine.

A little 3M Super Weatherstrip Adhesive will also hold them if you let it dry before you install the intake.