Having a vac on the crankcase is where I would focus. Well first I should ask how you checked this. When I checked my crankcase for pressure/vac, I plugged the TB/VC hose and removed and capped the hose from the pcv to upper intake. Then I was able to put the gauge on the pcv for an accurate reading. I will assume you did this, or something comparable.
If you do have a vac, even just slightly, that would suggest a leak between the intake and crankcase. I did have this happen to me a short time ago. When I had installed the lower intake the gasket had slipped down about .25" Can you visually verify that the gasket did not shift during installation?
Hope you get this sorted out soon
jason