Just to point out the obvious testing results, the initial testing showed FSH low, and the later labs showed ALT high (although not extreme) - however, ALT high and AST well within normal range, makes me wonder. Is he working out again? Additionally I would think a course of clomid at the lower dosages makes sense. While is T is reported on the low side, Estrogen seems to be coming in at normal levels (25 - although the test was likely the non-sensitive test which is scorned here). Otherwise, my guess is too much stress. You mentioned your own health issues (what may those be? not be too nosy, but the health of the partner does affect and impact the sexual response of the other), and vet school is very stressful.