I have a similar layout, around 3,800 sq feet on three levels. Z-Wave is indeed a solid recommendation to build the individual items on. GE's Jasc products (in wall outlets, in wall switches, adapter outlets are pretty good, I've got a bunch and I've yet to have an issue. Amazon usually has decent prices but be VERY careful about what switches you buy as three and four-way switches are not wired like you'd expect as one will be a normal switch and the others simply send a signal to that outlet - very different from traditional wiring.
For the hub, you'll want to evaluate what type of features you want. Do you want internet or smart phone connected (you probably do) - in which case take a look at SmartThings or Mi Casa Verde. The problem I've run into however is that if you want to tinker, not all products play well with other products. You can't use SmartThings to control Phillips Hue light bulbs for example - instead you have to integrate the bulbs into IFTTT.com's web service and then trigger them via the web via actions in SmartThings. Totally does work, but it adds a small amount of latency. When you flip a switch, you really do expect instant results and that 1/2 to 1 second is perceivable.
Another question is security, do you want open/close sensors on your doors and windows? Now is the time to wire it if you can and the wiring is thin and cheap. The z-wave wireless sensors you buy work, but do you really want to swap out batteries on a house that size? Plus, they seem unreasonably priced by my standard. Wired ones are 1/3 the going rate and are much more failure resistant.
You'll of course want ethernet around for your normal PCs, but make sure to add in a good location for wireless routers and put a few jacks where you'd want video cameras, even if you don't want to install them right now. Cable is cheap, rewiring isn't. Also, while Z-Wave products create their own mesh networks, the hubs that translate from Z-Wave to WiFi or ethernet need to have a good connection for them to work well. I find that I have to buy an extended range model to cover the house, but my location isn't ideal. That said, depending on your building materials you might need a repeater or two so an extra jack is a godsend when you need it. Keep in mind, you'll need a switch closet somewhere if you put a jack in each room. I ended up with 14 jacks coming into a bedroom simply due to poor planning regarding where the cable drop for internet ended up. I really should have put that in an actual wiring closest or something but too much was already dry walled before I got involved.
Schlage makes good door locks by the way. Tried a couple before ended up with them. PINs are so much easier to manage when I need someone to dogsit.
Audio: do you want centralized music/media controls? If so, it's easy now and a PITA later. Wireless exists, but latency is always an issue and SONOS is damned expensive.