The low coolant level could definitely be a clue! On your engine, there is a coolant passage in the rear of each cylinder head. The passage does not go through the intake manifold. The passages are sealed off by the lower intake manifold gasket. #5 and #6 intake runners are very close to the sealed off passages. The lower intake manifold gaskets are known to fail pretty regularly due to the inferior design. It's very possible for coolant to leak into the #5 and/or #6 cylinders if the gasket fails close to a runner. A cooling system pressure test may not reveal an external coolant leak, but may show a loss of pressure.... that would be coolant leaking internally. Coolant can leak into the runners or into the crankcase, or externally, or any combination of the 3. Felpro makes a greatly improved gasket set, (MS98002T) that will not leak if installed correctly. You might find that Autozone rents a cooling system pressure tester. If they do, perform the test when the engine is cold, and again when it's hot. Leaks can be tricky to find, and if you can't find any external leaks, chances are real good it's the lower intake manifold gasket. Keep us posted.