Ok, in that case, all you need to do is get yourself some pipe plugs and install them in place of the pipe nipple on the top of the waterpump and in the intake manifold where the heater hoses attached. Plugging off the heater hose points won't affect anything else.
The a/c side is its own deal. If you've removed the compressor, condenser, and all your hoses, all you're left with is plugging up the hole in the hvac box where everything went in. If you still have the vacuum lines in place for the a/c system, they will need to plugged off or removed as well.