You should not need any sealant on the flanges. First, make sure the intake and the exhaust flanges are flat. For the difference in thickness, use the oem clamps or the ones from Stovebolt and grind which side will be on the thick manifold to compensate. The modified clamp should put equal force on both manifolds. Also make sure you retighten the manifolds as they loosen up after a couple heat cycles.
Since you installed studs this is probably not needed, but make sure the end guide pins are placed with studs also.
