Your garage setup is similar to mine. I wanted significant garage space without the significant garage presence from the curb. We started our custom build job around June of 2001 and finally moved in November of 2002. While everything is fresh on the mind, I'll offer my $0.02.
Garage considerations:
Where are the beams that hold up the second story? What impact will they have on your available "clear" height and your ability to properly mount a GDO so as not to affect your "clear" height?
Make certain that your garage door tracks raise all the way to the ceiling and then turn at the ceiling. An 11' high ceiling in the garage is no good with a garage door that cuts in at 8' high. I have two garage door openings at 18' x 8' and 16' x 8', each with two extra dunage sections to allow the GDO to work properly. With the mass of the dunage sections, the physical doors are nearly 18' x 11' and 16' x 11'. I probably should have gone with commercial openers, but installed the 3/4 HP Craftsman GDO's instead. IIRC, my upgraded insulated doors and extra work to get this done were nearly $5,000 alone.
I'm sure you've thought of power requirements. I have 400 amp service with 2 200 amp Square D QO panels. Every circuit in my garage is 20 amp. I have numerous outlets in the ceiling for ceiling mounted cord reels as well as drop work lights on reels. There's a fair share of low voltage as well for shop TV's, phone, network, etc.
Also, with dual garages at a 90 degree angle from each other, be sure to plan for vehicle approach. We did a large sweeping "hammerhead" that works well.
That's my $0.02. If you want another dime or so on whole house construction and custom home builds, I'll throw it out there for you.
