Ohh...that sounds like a challenge! I had better break out my model kit.
I don't really have much more to add, unfortunately, and my knowledge of peptide chemistry is lacking. One thing I would add though is that the stereochemistry is very likely under thermodynamic control since the Michael addition is probably readily reversible. Therefore, everything can funnel to the observed diastereomer of product. Dan's argument is really based on kinetic protonation, which may (and probably does) control the first product that is formed, but if the reaction is reversible, then the epimeric product may form over time.* My guess is that you can find some 6-membered ring which is formed by intramolecular hydrogen bonding in the product. I'm very bad at identifying these sort of things however, but I bet it's there somewhere.** That's probably what controls the thermodynamic product. It is possible that the kinetic and thermodynamic product are the same, however.
* A useful experiment to determine whether the reaction is under thermodynamic control is to independently synthesize the other diastereomer of the product and then expose it to the reaction conditions. If it converts to the epimeric compound, then the process is reversible and dominated by thermodynamics. Cool, huh?
** In just glancing at the molecule, it seems that most of the obvious H bonds would make a ring where the isobutyl and the CH2SR groups are syn, which probably isn't favorable, so maybe I am missing something.