Jim, this is different from what I understood in your first post. The way that they did it in the change orders is reasonable, as we agree. But I agree that they have changed the deal and that you should get your lawyer involved. If you could have negotiated the 13%, or if it was in the contract, that would have been a "different animal". Since they didn't bother, apparently, there is no way that you should have to pay.
I wonder how any call-backs for things that you haven't caught yet or will not catch for a few years will be handled? Also wonder how they would have been handled if you don't gripe now? Did you ask the referrals that you checked with about this? You did check the builders references, right?