My 12 lb Jack Russell became extremley lethargic and anxious for 2 days following a rabies booster,distemper booster, and kennel cough vacine(nasal). Would it be better to have these vacines on separate visits? Which one would most likely cause this reaction?

Reactions aren't that common. It is hard to say which may have caused it. If you are going to have a problem, I doubt inconveniencing yourself and the greater expense of 3 visits will help.

More than likely, the reaction came from the bordatella, or kennel cough vaccine. This was the most common in the clinic I worked in. Was there a localized reaction at the vaccination site-redness, hair loss, swelling? Next year, consider giving the rabies booster only and go back after 1 week for the final vaccines. An injectable kennel cough may be a better way of administration for your dog. Just be sure and discuss this with your vet before any shots are given next time-they can also give pain relievers and benadryl before vaccinations to help him feel comfortable. Hope this helps!