Help! Intake manifold won't fit!

I use stock bolts and a 9/16" wrench on the 4 centers, torque the other 8 and tighten the 4 centers in steps, and feel the torqued ones with the wrench. retighten a few times after running. I did not do any machining when my intake was high - did not want to lower the ports and spend the money. put engine in and had my friend stand on intake