It can be really difficult to talk money with people, especially when they put up such a friendly, cheerful front. They make you feel like the bad guy for stuff they did wrong, and then you really feel like being a bastard about it now that you're feeling resentful as well.

Ahh...Fuck all that, here's my advice: I once had a career advisor teach me a non-confrontational way to raise money issues (and this works for asking for raises too): P.R.O.: Problem, Research, Options. In your case obviously the Problem is the extra costs you're taking on to finish the job. Research is, just list them in absolute terms of man hours and/or a quote you've gotten from another builder. Options: either they give you a reduced price, or if they think the other guy is cheaper than the price reduction you're asking, have the builder invoice them. Change the details as needed, you get the idea. Hope it helps.