Intake manifold help

Remove any roll pins on the china walls so the intake sits flush.
Then try pushing down on the intake a bit and see if things line up any better. If you get close and you still have the gaskets at the ends of the intake to block, remove those as well and use gasket adhesive in the gaskets place.
If you can not squeeze the intake on, talk to a machinist with pictures galore in hand.

Most machinists want everything there to work on and often shy away from guess machine work on something like this.

Try and get a better picture showing the misalignment directly overhead. Showing the walls of the intakes hole all around. Get all the hole pictures if you can but for certain, the 4 outter most on each corner.