First I would call it a custom home not a spec house. The idea of a spec house is to get it done quick & for less for the builder to put on the market to sell to an unknown buyer. Details are not so important.
A custom home is when the house is built for the homeowner the way they want it. They can take forever because of the constant changes the HO makes once it's half done. Also this can lead to disagreements about amouts due.
You could do a combination of flat rate and T&M. Flat rate on installing fixtures, fans, and devices. T&M on tracing/figuring out, checking, reworking, items.
