Hy 62Stick, over the years I have noticed the aftermarket oil pump drive shafts at all different depths in the gear itself, while I have never had an installation problem with any that I have installed, this is one thing I would check if I were assembling your engine and ran into this problem. While the block may have been decked, the intake manifold is still factory dimension and the distributor will not sit down on it, something is holding the distributor up. I would check the oil pump shaft height against a known good one to compare, if an adjustment to the shaft height needs to be made I believe the shaft is a press fit into the gear and as long as the shaft is not flush with the bottom of the gear there is room for "adjustment" of the shaft height, hope that helps.
