I dropped by Jake's house this evening to finalize some changes to our House Plan. We aren't changing a lot, but like everyone else there are a few little things here and there that need to be customized for our needs. One of the things we did was to adjust the master bathroom. We also changed a few of the closests since we have a lot of stuff. It's funny how a home that has been built for so many other people doesn't quite fit when you have the option to make a few changes. Of course those changes will add up to extra cash, but you have to pay more (sometimes a lot more) for custom work. Before you know it, the house is a lot bigger than the original plan and the price has gone way up. That is always the danger when you build a custom home. The compromises are fine for everyone else, but for your own home only the best will do. I would go with a 20% rule. Whatever price you start with add 20% for all the changes and little additions you will make. It isn't fun to admit that up front, but it will help you to plan for reality.
Best of luck finding and building your dream home.