Visit the house as much as you can while it’s being built so that you can catch things that go wrong (which there will be).
Absolutely! When the place I'm living in now was built, my dad went through the entire house and showed the wiring guy exactly what we wanted. Sadly, he was a few cards short of a deck, and completely screwed it up, despite a very clean, clear diagram from my dad. He put the rear speakers on the side of the room that the TV would be sitting, he neglected to put phone lines in the two upstairs bedrooms (thus my two roommates have been without phones in their rooms for 3 years), and according to another wiring guy, he screwed up the cat5 on every jack in the house. It works, but should be rewired.

So, things will go wrong, but it's nice to have a house in the end

Oh, and if my dad and I were building a house today, we'd go with good ol' Rich Trethewey's radiant heating. The main room has a cathedral ceiling and that makes it impossible to heat or cool.
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Matt