Ditto the above. If you had the heads resurfaced, it affects the clearance and alignment on the lower intake. You're an autocad guy - you can visualize why. We used to have this trouble on small block Chebbies, and we used to have a lesser amount than the head cut taken off the manifold flange, calculated from the trig of the angles.

I'll add this to FrankR's comment (hi, Frank, long time no talk), I do the torque down in steps, tapping the intake with a dead blow in between steps to settle the intake into the vee.

While you have the lower intake off, check the oring on the water pump end of the steel pipe.