One of the things to keep in mind when building a new house is that it seems like almost everything is "extra".

An example is kitchen cabinets. Picked out good quality Merillat (sp?) cabinets but as they were being installed I asked about the door and drawer pulls (handles), where were they? The answer was those are "extra"....not part of the drawers etc...????  Ended up costing several hundred dollars more for drawer, cabinet and some closet door pulls and installation.

A well around here is going to cost a lot more than $3500 since they generally need to be steel cased down over 220 ft and a total depth of 300-350 ft in rock. $12,000 + would be closer.

Contractors will leave many things out of the quote to keep the price down so they get the job. It is just the way that industry works.  Just figure the house will, in the end, cost maybe 25% more than your highest initial estimate because of things that come up during construction and "extras".

A friend in the business says he sees folks that arrange a mortgage for a quoted amount then find that amount is really not sufficient...causes lots of grief.  Figure it will cost more than any quote you receive.

Good luck.

Jim