1) discrete codes come from the original equipment, and Sony tends to have them. The Harmony can learn them, but you need a remote with them to tech it.
I have a Sony 34XBR800 (which doesn't appear to be in the DB, incidentally)
exact models for my equipment did not exist either, but most similar equipment from the same manufacturer tend to use the same codes.
Will I be able to program it to know that "Watch DVD" is input 5, while "Watch HDTV" is input 6?
yes, the harmony also keeps track of stuff so even without direct input, it would know 6 is one input from 5
3) the build of the original Harmony is not bad, but from what I heard, the new one is much better (just ordered my upgrade)