Eh, the program's easy enough to adjust when necessary. Just need to see v6 of the Challenge Ratings appendix, and whatever final method you come up with.
On that note, the Neutronium Golem's extra power relative to the Leviathan comes from two places: first, its bigger hit die, and second, its extra VSCs. Perhaps those need to figure in to the calculation of "HD Modifier" somehow, to determine what portion of the EL is "kept back" for the recursive part of the calculation? For example, I'd certainly call a d1000 hit die more powerful than a d10 hit die, which is what normal Constructs get. So perhaps the multiplier of 0.35 isn't correct. Of course, this would mean the Orichalcum Leviathan's multiplier is higher too, though not as high as the neutron star, since it gets d100.
I do understand that they're abilities of the various divine tiers, but I'm just saying maybe their addition to CR adds more than once (in effect), unlike other such abilities.