Well, there's generally a clause in building agreements that the work will be done in a "good and workmanlike manner" and that where different materials are used they will be of least as good quality as the original spec, or higher. You could argue that dropping the spec, and the water damage (if they are serious enough) means that they are in breach of the terms of the contract, allowing you to rescind, and walk away (possibly able to sue for the return of the deposit).
How that would turn out largely depends on the extent of the defects, but it's worth looking into.