Ill Fitting Tunnel Ram Help

Hey everyone. I'm helping a buddy put a Weiand #5987 tunnel ram on his 440 and he's run into a bit of a snag. When he went to bolt it down, it seems as if the angles are a little off? He had a hard time starting several of the bolts and it isn't pulling down straight as it should. Let me tell you all that I know and maybe you could shed some light on the situation.

The engine was rebuilt within the last five years using Edelbrock heads and intake and has been a driven several thousand miles. This is a show/cruise night type of car. My buddy wanted to increase the WOW factor and has always wanted to add a tunnel ram. A couple of months ago we found a NOS Weiand intake at a swap meet and the dream started to become a reality. It appeared to be never bolted onto an engine with no obvious damage.

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We mocked everything up and didn't notice anything out of the ordinary? We worked on the fuel lines, throttle and kickdown cables. Everything seemed to be going along fine. Although now I notice in the picture below, he only had a few of the bolts started on the intake.

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When he went to do the final assembly he had a really hard time starting all of the ARP intake bolts. After what seemed like hours of trying different orders and combinations he thought he had them all started. After he started tightening them, he realized that something was not right. They were getting tight (binding) before the washers even hit the manifold. Here's a pic of the driver's side.

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But now look at the passenger side. It appears that the angles are off and there is no squish on the Felpro #96007 gasket.

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My question to the group is, how are we going to correct this? As far as we know, none of the surfaces have been cut or milled with the exception of maybe the block. We are not opposed to taking the manifold to a machine shop to have it's angles corrected, but need know how to go about figuring things out.

We are both mechanically competent but not highly technical mechanics working out of a one car garage using basic hand tools. Just two old guys working on old Mopars. Thanks in advance for any help or guidance you can provide!