Anyway; For the most part, this is making sense, though it'd take a huge amount of energy from
somewhere to execute the transformation itself. More on that later. I imagine the infection process would be pretty much as Curan described; the virus would go in and modify the new system, adding and changing things, but not replacing it all. Perhaps the source of the virus would have some influence on the traits of the resultant werewolf, or perhaps the virus would make the changes independant of wherever it came from, working solely from the genetic makeup of the new body, sort of like a procedural filter in Photoshop. I favor the latter, but it's close.
Back to the transformation itself. All that energy for moving things around, and possibly getting more matter, has to come from somewhere. From Einstein's equations, we know that matter and energy can be converted to eachother; scuch a process is, in fact, used in nuclear reactors. Given some VERY weird biological structures, I suppose that transformation to a lower-massed body could be powered by fusion, and the energy from that stored somehow for transformation back. However, even this leaves the question of where energy and/or matter for higher-mass transformations come from; namely, to the gestalt form. Assuming near-100% efficiency in both the transformation and the storage of energy, perhaps this is why the first transformation is typically the hardest/most painful, and effects the human form (raising health; removal of much fat, plus encouraging the body to be more vital in its reconstruction of lost tissue) so quickly; the necessary energy could be gathered from body fats and various other non-vital tissues, combined with, perhaps, a small store of energy transferred from the WW who did the biting. Add to that the possibility that the first transformation to a higher-mass form is significantly impaired the first few times (weaker, smaller by a small factor), until enough energy has been garnered over time from things such as the digestive process, and you have a plausable explanation. Except for how the transformation itself is executed, but for now I'll attribute that to some more specialized modifications and leave it to someone else to add detail.
Time to get back to my homework

Sanity is relative.