On the 1200 square foot minimum bit...
Make it bigger. You don't have to make it significantly more expensive. Too many houses have dinky bedrooms, etc., and that really hurts them. If you're able to do your own interior work, you're set right there. Drywall, floors, etc... If you're putting it on a slab (I'd prefer a basement...), tile is easy. Think radiant or environmentally friendly stuff too. If that stream has enough throughput, consider a small hydro setup. Lower energy bills and tax advantages.
If you're good with tools, you can put together a NICE kitchen for about 10% of what you'd spend on the pre-built cabinets. Likewise for other areas of the house - built-in bookcases, closet areas, etc., are so much easier when there's nothing there.
If you design it so that it can easily "stretched" with an addition, that's a plus too... I'd like to build onto my house here, but the dang gas line is right where I'd like to put it...