Mmmm. There are a shelf full of BHSE, just aching to be shipped, and folks are still wailing at Justin. When you hear all the "special needs" going on, I can see why Justin has troubles answering his emails/PMs, etc. As for changing your order now?
I know this is an expensive, custom project, but this is an expensive custom project, and I am pretty sure he goes by your wishes when you ordered. I myself did not order plain vanilla, but I knew when I signed on way back when that it would not be delivered until it was ready, and that it would take awhile. Justin did send a couple emails about what I was wanting, and did seem to know what I had ordered initially. It was confirmed again when I submitted the final payment.
As to the tubes, those units look to be just finished testing, during which I am sure he uses his standard tubes, so the measuring would be uniform. I think that he will remove those tubes, install the top, then pack the units for shipping. Tubes, cables, and possibly feet, will be installed by the new owner.