Sorry to hear of your problems.  A lot of responses.  I want to add that some of the issues you ran into would be avoided with a panelized home rather than stick built.  Can be a custom design but 4 page signed and architect/engineer approved blueprints are sent to a panelizing company and they engineer and build it in panels, truck to your foundation site and your contractor puts it together there. We did this 5 years ago and I could not be more pleased with the results... I just don't want to ever go through that again!

A very important point you have made is that no matter what construction or who is doing it, you really need to be there, with a copy of the blue prints the contractor(s) quoted on, almost full time while the work is being done, especially at critical stages such as digging the footings pouring the foundation, installing inside and outside the foundation drainage systems, pouring the basement floor, etc.

If the prints require the basement floor to be 4" thick and have rebar every 24" over a compacted gravel base, you really need to be there as it's poured, with a tape measure. Shouldn't be that way but unfortunately often is.

There is also no substitute for a good general contractor and good subcontractors. Don't be afraid to speak up during construction. It's now or never in many situations. And if you always take the low bidder there is often a reason he is the low bidder.  Find contractors and subs with an excellent reputation and satisfied customers.  They will usually NOT be the low bidder.

There is a recent sequence of shows on "This Old House" showing the panelized process on a home in New England. Some of it is over the top but the earlier episodes on foundation and erecting panels are very useful.