Help! Intake manifold won't fit!

That looks close enough. Delete the front and rear gaskets and use gasket maker instead that should get you low enough to get the bolts started. Get one side started and force the other side down. The intake has to "wedge" in your working with a V shaped opening. If all the holes lined up perfectly just setting there it would never seal correctly and you would end up drawing the intake sides to the heads and something would either bend or break. You're gong to have to force it down some.