Steve,
If you haven't done this already, try placing the manifold on the block without any gaskets or bolts and check to see if the head and manifold gasket surfaces are parallel (top to bottom). If necessary, slide the manifold toward one head to lessen the gap and hand thread a couple of bolts for alignment...repeat for the other head.
You might be able to get better sealing by using 0.125" intake gaskets.
John