Nice experimental step. :)
I think that uneven spacing is the fundamental problem. I remain convinced that the top and bottom groups of portholes are at 11 o'clock and 6 o'clock respectively, but the other three visible groups are clearly bunched up rather than evenly spaced. However, since one group has three covered portholes that are clearly different to all the others, the craft is definately NOT symetrical, so what's happening on the other side will always be a matter of speculation. My feeling is that there are two groups of four portholes around there, for a total of seven, but there's no way of 'proving' that.
Re the tentacle dome, looking at the picture again, I get the impression that the hole in the yellow disc is actually bigger than the dome, and that the latter sits inside it at such a height that if you looked at it edge-on, about half the diameter of the yellow dots around it's edge would be visible. This is why it the dome looks taller in the pic than in your model: in the former, you're looking down 'into the hole' it sits in so you're seeing more of it's height.