The machine shop mentioned something along those lines early on in our discussions. He currently wants pictures to see if the intake mounting bolts were contacting the mounting holes in the intake and they were. I just sent those pictures off last night.
However, the engine is currently in the car and an hour away from the machine shop. I hope the machine shop has a better way to measure the angle difference than just an "eye balling" because currently I dont have a way to get the engine out and too him.