(4) Current plans call for a central closet on the second floor. Should all the cables run to that room or to the home theater system in the living room? There isn't a main closet near that room, unfortunately.
That is the key to it all. New homes with 'structured wiring' are configured in just that way. Mine is in the master bathroom closet.
Every room will have whatever cables you need (RG6 for cable/satellite, CAT5e for phone/network, and various speaker wires). The RG6 and CAT5e go to the central wiring closet where there should be a phone patch panel and/or network switch). The speaker wires go from the speakers in each room to the location of the HT equipment. If you want multiple speakers around the house you need a multi-zone receiver or a combination of speaker selector and impedance matching volume controls - it all depends on how many pairs and whether you want fully independent source and volume control for each room.
My house was fairly well wired but required upgrades. I would recommend at minimum 2 RG6 and 2 CAT5e to each room so you can have cable/sat and phone/network in every room. With the patch panel and network switch in the central wiring closet you can change any jack from phone to network simply by switching the cable from the phone panel to the switch or vice versa.
Your builder may offer structured wiring as an option. It is much easier to do it before the drywall goes up than to retrofit it afterwards.
That's the short story...but I can explain how I've got my house wired if that would help you understand some of the options.
Edit: And don't shoot yourself in the foot. Be sure to run CAT5e cables for network to a location near your HT equipment. Lots of current and future devices will need access to your local network and/or the internet for full functionality.