I am pretty sure it is the result of the mock up moving during shipping. For example, the tube for cylinder #2 seems to have moved closer towards the valve cover at the turn down towards the collector. I struggled getting the mock up rigid enough to prevent movement in this area during its construction. It doesn't take much movement at the header flange to make a big difference 8-12 inches away from that point.
The PVC was touching the starter when I did the mock up. I had hoped that the difference in O.D. between the schedule 40 pvc and the 1 7/8" primary tubes of the final product would provide sufficient clearance. It would have been very tight under the best of circumstances. I had figured on possibly having to dimple a bit. I had the UPS store package the mock up for shipment, so I did not control that part of it.
I have since dimpled the tube for the starter clearance, and may contact the fabricator tomorrow to see about modifying the header. It isn't bad at this point, and I am not sure it is worth the hassle. In short, I would do it again, but probably would consider making a jig to hold the mockup securely for shipping to ensure no movement. I considered it prior to sending this set, but got in a hurry/lazy.