I have to say that on the whole, your system modeling seems pretty good, given what we know at the moment. (Extrasolar planets are a hobby of mine. I've read a lot of the literature.) I've yet to see any hot Jupiters, but we don't really know how common they are yet; Kepler should tell us in a few years.
I have a few issues with the treatment of habitable (and inhabited!) planets, but this probably isn't the thread for it.