Manifold doesn't line up

Plain and simple, the gaskets take up space and raise the intake. If the bolt holes are off and you can lift the intake a 1/8" or so to align the holes then all is well. And like everybody said, toss the end seals and use Right Stuff instead. Clean and dry both surfaces, apply a good sized bead to the China wall and the edges where the gaskets are, bolt down the intake, torque as needed and walk away. No fluids or engine running until the next day. Let it set up. Good luck.