I would recommend the following as a minimum:
Differential cell count (neutrophil/lymphocyte ratio often used as indicator of stress).
Cortisol (classic response to nutritional and environmental stress). NEFA (Non-esterified fatty Acids; an indicator of nutritional insufficiency, also responds to stress). Glucose (changes markedly as digestion shifts to rumen).
Urea (changes markedly with onset of ruminal fermentation and breakdown of dietary protein)
In addition, a satisfactory environment for a calf provides thermal and physical comfort, plus minimal disease. The thermal neutral zone in the calf is 50 to 85 F in still air. So watch for signs of decrease intake that would reduce calf health and growth. Naturally, cleanliness and stocking density can affect the pathogen challenge to the calf. Monitor body temperature and watch for clinical sign about the muzzle and eyes. Don't overlook the handler(s). One stressor which is easily eliminated is the improper handling of calves by caretakers which can cause both behavioral and physiological stress effects.
James K. Drackley
Professor of Animal Sciences
University of Illinois - Illini DairyNET
J.W. Schroeder, NDSU dairy Extension.