I figured a few things were wrong, as the modeling wasn't quite accurate when I was testing last night, and i see where i misplaced a decimal place on neddra's influence. I also thought that all bonuses were moved from multiplicative to additive, regardless of the source, so all buffs would be added together and then all debuffs added together. I'll have to test that tonight, but you may be right and they never changed that. Lastly, I now see where I made the mistake of 1 stack vs 3 stacks. It is obvious to me now that the damage is calculated based on 1 stack and then multiplied by how many stacks there are. Appreciate the help. Spreadsheet updated!
And I concur that Shaely's parse is indeed not legit after running all the numbers. It is impossible to hit the numbers he was hitting at our gear level without manipulating synergy crystals.