For those considering making a cat a barn cat, it is important that the cat be caged (in a large dog carrier) for at least 2 weeks (most cat rescue agencies recommend 3-4 weeks) in the barn, with ample food and water, and litter box. Otherwise they will likely just panic and run and be lost and...
Great overview Cara!
A couple things Warren Eckstein would likely recommend (and they need not be permanent once things calm down, assuming they do), and assuming medical causes are not at issue:
A few litter boxes scattered about in his area, kept - as you already do - cleared of pee/poop...
A lot of great suggestions above. I tried to answer when you first posted and right then and there my mouse died! Computer mouse that is. Just got back from shopping for a new one.
Anyhow, if you'd like to speak to an animal behaviorist for free, check out www.thepetshow.com and you can call...