Let this thought burn itself into your brain: THERE ARE NO SHORTCUTS IN ESTIMATING.
Looking back on the last home I wired ... a custom like the one you describe ... here are a few 'lesser' points to keep in mind:
1) Without at least a floor plan, the guy doesn't get the time of day;
2) As mentioned in another thread, no quote, plan, or estimate without either a contract, or payment for your efforts;
3) You're going to have to design it, add up your costs, and give a total price. Based on those figures, you can also develop figures for making changes (for example, $120 for each additional device, or a saving of $60 for each device deleted).
Get some prints, and look carefully at the structural details- especially above the ceiling. Can you access those spaces? Is there a hatch to each section? Do the trusses prevent you from moving about? Be crystal clear, even vlunt, regarding the impossibility of making certain changes once the rock is hung.
Local CC&R's can have a major effect. For example, in the house I did the service had to be installed flush to the outside face - which made certain tasks a lot harder.
As a 'custom' house, you can forget about just placing a receptacle every 12 ft., a light in the ceiling, and a phone in the kitchen. You really have to look at the intended uses of the rooms, specific to the customer.
You'll want a large Jobox, or even make a small shed, on site for the storage of your materials. You really don't want those 1000 ft. rolls of Romex to shrink in the night.
Figure into your bid costs for heating the site, and supplying temporary power. (In my case, I was able to temp in some receptacles in the garage, and power them from the main panel).
In the house I did, I ended up using four sub-panels, in addition to the 'main.' With hindsight, that probably should have been five or six! Think it over carefully.
You'll almost certainly be installing a 'structured wiring' cabinet. Required circuits are likely to include many that you would not normally think of: central alarm system, central vacuum, etc. Look at that appliance schedule real carefully.
I also strongly reccomend that you run a 1" pipe under every concrete slab, drive, or patio. I guarantee that you will later be asked to install a pond, or some such.
The main thing is that you have a real good chat with the occupants of the home: what are their expectations? What is their desired lifestyle? Then break out the crystal ball, and design to their expectations as best you can.
