That is one nice little shop there, someday maybe I will be so lucky! We have a joke int he shop at work that the perfect retirement home would be 500 square feet with a 50,000 square foot shop attached. One can dream. Here though it looks like a dream come true.
As for the second story / loft area do you have specific plans for that area. I looks like the perfect place to put Air compressors, HVAC, and other equipment that can clutter up a shop floor. My "shop" is in the basement at the moment and thus have plenty of experience with other things cluttering up the work place.