Intake manifold/cylinder head internal vacuum leak
Occasionally, you may experience a vacuum leak into the intake ports from the crankcase of the motor, due to the intake manifold/cylinder head interface not being machined parallel.
For example, consider looking at the manifold from an end view, from the front or rear of the car. Unless you're using all brand new parts, you have no way of knowing if the heads, block, or manifold have been machined by the previous owner, so the interface at the manifold/head could be out of parallel. In other words, the gasket might be pinched tightly at the top of the port and sealing fine, but might be wide open to the crankcase at the bottom of the port, allowing oily vapors to be drawn into the intake manifold runner on the intake stroke. The manifold may also be warped a little. No amount of propane or carburetor cleaner will find such a leak due to the leak being on the bottom of the port, where the combustable agent cannot reach. The best way is to insure the elimination of such a problem while building the motor.
Not all cylinder blocks are cut squarely
Be aware also, that not all cylinder blocks are cut squarely to the centerline of the main bearing bore on the block decks, so if your decks run uphill one way or the other from one end of the block to the other, you can see how the cylinder head would not be square to the centerline of the main bearing bore, and could create a condition where the intake manifold would not sit squarely against the heads. This is a very good reason to cut the block decks square to the main bearing bore before you ever start building the rest of the motor. The other reason to cut the block decks is to set your piston deck height the same from one end of the block to the other. Add up your stack of parts (1/2 stroke, rod length and piston compression height). Example on 350 Chevy: 1/2 of the 3.480" stroke is 1.740", rod length is 5.703", piston compression height is 1.560". Added together, the stack in this case is 9.003, so if you wished to run zero deck with a 0.040" gasket, you would cut the block deck height to 9.003".
Setting up intake manifold/cylinder head interface
Here's one way to set up the intake manifold/cylinder head interface to prevent vacuum leaks from the crankcase to the head ports:
Begin with the heads properly torqued to the block for the final time, and ready to go. Measure the thickness of your new intake manifold gaskets. Get flat washers or shims that will measure that thickness. With the manifold off and the mating surface on the cylinder heads degreased, put a dab of RTV on the washers/shims and stick them on each corner bolt hole on the cylinder heads. Let the RTV set up. Stuff paper towels into the ports to keep debris out. Make up 16 BB-sized balls of modeling clay. (Use oil-based modeling clay from a craft store, not Play-Doh). De-grease the intake manifold at the ports. Place the balls of clay on the top and bottom of each port of the manifold, squishing them down well so they stay in place. You want them to be thicker than the shims/washers that are RTV'd to the heads. With your fingers, coat a little oil on the heads where the clay will meet the heads to keep it from sticking to the heads. Now carefully place the manifold into place on the heads, and use bolts on the four corners to just snug the manifold down until you feel resistance against the shims/washers. Remove the manifold carefully. Cut half the clay away at each position with a pocket knife. Measure the thickness of the remaining clay at all 16 positions with the depth function end of your 6" dial caliper. You'll know pretty quickly if the manifold/head interface is square. Record the measurements on the manifold with a permanent marker. The widest measurement will be the standard to which you will want your machinist to cut the other positions on the manifold to make it square with the heads, thus sealing up the motor.
Pay particular attention to interference at the bottom of the manifold at the block rails, front and rear. If you cut the manifold, you'll be dropping it down a little into the valley, so pay attention. Also, with the manifold down a little in relation to the head ports, the ports may not line up exactly. On a street motor, don't be overly concerned about it because, physics dictates that the majority of the flow is right down the middle of the port and the surfaces of the port wall will be relatively slow moving. However, if you want to be perfect on your build, you should port match to the gasket. Also, using two gaskets on each side may line things up better without any need to grind on the ports.