No matter what the plans say

"Thats the way we do it"!

So you work very hard with your architect and get the plans carefully thought out, drawn up and approved.  Now you are dealing with the builder.  Each builder has "his" way of doing things.  The architect should have provided you with specific detail as to how the windows and doors  are to be fitted for example.  Also how and where the plumbing and electrical are to be run.  How the roof structure is attached to the walls etc etc.  The builder and or his guys have their way - "the way we always do it".  You need to be aware of this little sublety and try to deal with it tactfully.  There is a very good chance the artichect has detailed the "correct" way as opposed to the way "we always do it".  Welcome to the real world of construction.  Even in Canada at times the guys thought they new best but after they tried it the right way a few times they actually realized the archetects actually know a thing or three.  Discuss these details with the architect and get his/her reasoning so you completely understand.  It's hard to challenge "the way we always do it" unless you know why.
Pay close attention to the rough opening for doors for example.  There is nothing like trying to get into the bathroom sideways.  

- Gutter flashing?
- Placement of septic tank?
- vapor barrier under floor slab?
- Packed gravel under foundation wall?
- Hight of slab above grade?
- Plumbing and electrical runs?
- Wiring gauge - "they will never notice" ?

If you detail it and detail it again with the architect you will have half a chance of things working out close to what you had hoped for.  When you are discussing with the architect there are no dumb questions.  You are paying him/her for their knowledge of local building issues so ask the questions and keep asking until you are happy with the answers.

 So think about it

These are just a very few random things that you need to consider in planning the project so think about it carefully. Very carefully.  Are you ready for all this?