I prefer checking without gaskets just because it's easier to "see" how bad it is or not and better for an accurate measurement. With no gaskets, do not install bolts or snug, just let the manifold sit on top. Also, very important to make sure that the bottom of the intake runners are not being held up on top of the head gasket tabs. I make it a habit to just bend them over with a small rubber mallet after the heads are torqued. After I check and/or adjust the intake face angles with no gaskets, then I dry install the gaskets and check for valve cover rail alignment.
Also, during this whole process, make sure the distributor hole is still centered...