I am in the process of building a new house and my builder is CLUELESS about home theater. After a little research this system would be in a 30x30x12 room.
Wow, I don't mean to be condescending, but why, with the obvious amount of money your sinking into your HT, would you even consider allowing someone less than an expert design/build the room (or house for that matter).
In those same magazines you've perused for your equipment choices I'm sure you've seen the advice to have your HT room professionally designed. That is because the design, treatments, and component placement are very important issues for high end systems. You'd be better off to by an HTIB if this your direction. Poor acoustics can't be fixed by spending more on equipment.
Structured wiring and home automation are another area that should not be left to the ignorant (no disrespect to your builder). I've seen a number of systems reduced to maintenance headaches and lost dreams (and $$$) due to ill-advised installations.
You've done a good job with the gear, now do yourself a favor and get yourself some pro help so you can really enjoy your investment!