For follow-up discussion and general commentary on the topic. Comments are sorted chronologically.
It seems to me that the simple answer to question about food and manure could be more easily understood if some form of hibernation were involved for most of the year they were on the Ark. We currently see this with bears and many other forms of life and certainly God could have, if He chose, to provided for their life being protected by some thing similar to hibernation.
The Answers in Genesis organization built a full scale replica of the Ark (in northern Kentucky). The three levels of exhibits demonstrate the "How" of the Genesis account including addressing flood science. It's a scientifically compelling and a spiritually faith building experience!