Building a home, need your thoughts.

Hey guys,
I know I'm new here but I've been search these forums for a little while and have always wanted to do a DIY home automation. Well the time has come for me to start making decisions fast as my framing goes up on monday, and I'm looking for advice. Let me just start with listing my goals:
Home automation present goals:
- Control lighting (rope, sconces, ceiling star field) in dedicated theater room
- Control AVR, projector, future anamorphic lens, etc
- Everything controlled by multiple IPADs
- AVR will have multizoned audio, so ability to music via ipad
- I plan on placing a couple IP camera systems on exterior of house (upgrade to more IP cameras eventually)
- Ability to control wireless switches/dimmers
Home automation future goals:
- More IP cameras (DVR capability?)
- Weather station
- Garage door/locks (maybe)
- Motorized curtains for home theater
I need to make decision on wireless switches, dimmers, outlets. I plan on running Cat6 to essentially every room in the house, as well as to soffits on exterior. I also need to make decisions on the home automation controller. Originally I had seen demos of Control4 and thought it looked really neat. Then I found out that its not entirely DIY friendly.
I'm looking for advice on:
1. Home automation control systems based on my goal (CQC, Elve, RedEye, ???).
2. Things to make sure I get done before sheetrock goes up.
3. Suggestions of wireless switches that work well with suggestion in #1. (Lutron, Insteon, X10, ???)
4. Do I need a HTPC to serve up my media or does home automation control do that?
4. Anything I should also research ???
I am a newbie to this subject but I am technically competant. I'm an electrical engineer by trade, I have lots of familiarity in Linux/networking/programming/circuit design etc.
Sorry if this isn't the correct forum to post in.
Thanks!, Josh
Welcome.  Before answering I'll just point you to some recent posts that will give you a lot of the information you are looking for.  After reading those, you will have a better understanding of what you need to do before the sheet rock goes up as well as some of the options that are out there.  You could then ask more specific questions as the one thing about DIY is that you are the glue that puts the system together and there are a variety of ways to meet your requirements.
By the way, I'm not trying to punt on your questions, I just know that various permutations of your post have been answered.  As a matter of fact, these are all from my recent post history.  When you have time, I'd suggest you read through these discussions to give us a kick start on narrowing down what's important to you.  I will say the most important thing for you to focus on right now is the wiring, wiring locations, and conduit.
Thanks David,

After I posted that message I kept reading and you are right I did find a number of people posting just like me. I will continue to read those thoroughly and get back with specific questions.