Bryson:
I agree with Brian. Also, I wouldn't worry about heat loss through the joists and spacers in the second layer. You will lose some heat no matter what you do. Brian's suggestion to use 2x4s and ISO panels faced with OSB will take care of most of it. Also, the ones I have seen come with lateral recesses in either 16" or 24" OC so you can apply them like sheets of decking and acheive the desired R factor. Then you put on your vapor barrier and roofing materials.
As to the critters, there is no getting around them. I would use some hardware cloth strips wide enough to bend and come up at least a little ways on the sides of the joists on each side and fold up the full height on the bottom and top ends. If you get the 1/4" HWC, it will prevent a lot of the furry little beasts from making your home their home. I would do this in the floor and the roof. I am aware that it is an added expense as well as an expenditure of extra energy and time, but it will pay you dividends in the long run, and that's what timber framing is all about, isn't it?

Keith in Houston