Get everything spotlessly clean and be sure to clean up all gasket debris from the lifter valley.  A shop vac works well to suck any gasket pieces from the lifter valley and from the intake ports.

Remove the old manifold and clean up all the mating surfaces.  Finish by wiping clean with carb cleaner or other non-greasy solvent.

Take these cork (or rubber) end seals and throw them in the trash can. They are NOT to be used in this installation!

It is best to use brass threaded inserts in your aluminum manifold. It will keep the sending units and hose fittings from seizing in the aluminum.

Clean up the thermostat housing as well. Take some gasket adhesive and glue the thermostat in place as shown. This will make it much easier to install it on the manifold. Note thermostat direction. IT MATTERS!

If you are installing early 351W heads on a 289, 302 or 5.0 engine, take note of the water port differences and gasket requirements.  
You MUST use the correct 351W gaskets on the early heads or you will get four major water leaks! The early 351W intakes had 4 extra bolts that went through the 4 water jackets.

Place a bead of RTV on each end of the block as
shown.  Notice about how thick the bead is.  Smooth it
slightly to remove any lumps.  Put a little extra in the
corners.

Be sure the water ports on each end of the gaskets are properly sized.  There are different sizes of intake gaskets for 289/302/5.0/351W engines.  

A mismatch will cause a major water leak!

Apply a paper thin layer of black weatherstrip adhesive or gasket adhesive on the “head” side of the intake gaskets.  Do the same on the heads where the gaskets will mate up.  Notice the tab on the bottom of the intake gasket.  That tab is designed to hook over the head gaskets.  Trial fit before gluing!

Once the paper thin layer of adhesive has completely dried, THEN place the gasket onto the heads.  The adhesive will stick immediately,so be sure you get the gasket in the right spot the first time.  Once the gasket is glued to the head, apply a paper thin layer of RTV to the surface of the intake gasket that will fit against the intake manifold.

Clean the intake mating surfaces thoroughly. Coat ALL mating surfaces on the bottom of the intake manifold, including the end seal areas, with a paper thin layer of RTV.  This will make for a 100% seal once the manifold is placed on the engine.

This is a view of the rear intake seal with a thick bead of RTV and the intake gaskets after coating them with a thin layer of RTV.

Place the intake on the engine using 4 alignment studs screwed first  into the heads.  The studs will be removed after some of the intake bolts are in place.   The studs will keep the intake from sliding on the RTV surface and will properly align the manifold to the heads

Torque all bolts to specifications in a circular pattern starting from the center bolts and working out to the ends. Retorque 3 times.  Let the RTV cure overnight before starting engine for best results.

Now install the distributor and carb and neatly install the plug wires.
Make a steel tubing line from the fuel pump to the carb inlet.
Taking extra time to do it right will make a big difference in the way things appear (and function) under the hood.