We do not have to consider the load bearing and non-load bearing parts seperately, because these can be bundled together as one dimension as what matters is the ability of the dimension as a whole to support the third dimension.
The formula then for making a 12ft giant is therefore 2*4*4, is this mathematically correct?
No, no, you're still oversimplifying. If you have a steel flagpole, doubling its height will always double the stress from its own weight on it, even if you increase its thickness at the same time; the decrease of gravity with altitude notwithstanding, a tower of any certain material would always collapse on itself after reaching a certain height regardless of how thick you make it. Likewise, doubling the height of a creature will always double the stress on its load bearing parts, no matter how much thicker you make them.
The trick to all this is since creatures aren't made of only structural parts, and that increasing thickness increases what load can be supported beyond their own weight; in your 2x4x4 proposal, the non-structural parts would be causing twice the stress as in a normal creature, but if non-structural parts only increased by 2x2√2x2√2 while the structural parts still increased by 2x4x4, then they would be producing the same stress as in a normal creature. There could be another amount the non-structural could increase that would cause the total stress to be the same, but the fact that you need several non-structural parts to live severely complicates things.
You want a simple answer to "how much does a 12 foot man weigh?" Well, the largest polar bear ever caught was 11' 1" on his back legs and weighed 1002 kilograms, so 1002 Urists x (12/11)^3 = 1301 Urists should be about right. Not sure what that is for size, but you have access to wikipedia and dwarfortress wiki, so I'm sure you can figure it out using the average size of polar bears.