To ensure the intake valves are closed, you have to start off with manually turning the crankshaft pulley to TDC. Once you do that, insert a long screwdriver or dowel into cylinder 1 and note the height of it. Insert it to the other cylinders, compare the height and and you'll see differences. An old school method is to leave the screwdriver or dowel in place and while turning the crankshaft pulley, you'll see the screwdriver or dowel rise up (closed) or drop down (open).
To thoroughly clean the intake manifold, spray brake cleaner, throttle body cleaner, etc into the intake ports on top of the intake manifold where the PCV hoses connect to. Also, where the MAP sensor plugs into the rear of the intake manifold. You'll also notice next to the MAP sensor location is another port that is plugged up. Remove that and spray away. There's going to be a lot more residual oil that will drain out from the intake manifold.