Intake manifold won't seal - How do I check it ?

Simple procedure. Here's how you do it. You will need two tools. A short bullet level and a dial type angle finder. Harbor Freight has both on the cheap. First, whether the engine is on a stand or in the car does not matter. Level the engine up from front to back. You need to cut a straight section of 2x4 long enough to span the intake valley front to back. Lay the 2x4 sideways on the block parallel with the crankshaft. Get your level and put it on the 2x4 and level the engine up front to back.

Next, put the level on the front block face where the intake meets where you would normally run a bead of RTV to seal it. Level the engine upside to side. Double check the front to back measurement and make any necessary corrections. Might want to double check the side to side if you make corrections. After it is good and level both ways, take your angle finder and measure the angle of the intake face and write that number down.

Now that you have the cylinder head intake face angle, time to move onto the intake. Flip it upside down on some good level concrete. Get it level front to back and side to side just like you did the engine and find the intake face angle. Write that number down.

The angles may not be different. All that maybe wrong is the heads and or block may have been milled at some point in the past. You can find that out, too. Take the intake and place it on the engine with gaskets in place. Line up the intake bolt holes. If they do not line up in the center of the intake bolt holes of the intake, the heads and or block have likely been milled. Remove the gaskets and try it again. If the holes are good and close to or on center, there's your answer. Mic the intake gaskets and have the intake milled however thick the gaskets are to whatever angle your first angle was for the engine and your problem is solved.