Personally, I think the sentence makes more sense with the addition of one more word, "does", after mouse.

"And so I'd guess that where we cost more than a mouse does is in putting a bigger fraction of our energy into self-repair, and a smaller fraction into other purposes like keeping warm or caring for babies."

Then again, looking closer I think that "in putting" needs to be changed to "that we put" in order to be correctly grammatical.