I'll second what goldielocks said about book keeping. I started a thread in the tax forum about determining cost basis on my house because I kept poor (read:none) records of expenditures, it definitely puts me in a bad spot with tax choices.
To answer your question, the first house was a simple ranch, slab on grade, 3/2/2 1300 square feet of house and 620 of garage. One story is nice because it allows you to do most of the work with fewer ladders and less risk of falling or dropping and destroying tools. I diy'd in floor heat using a company called randiantec out of Vermont. I think they're still around, the system works great, although it doesn't meet local code (will only require minor modifications to do so).
As far as the permitting goes, I can't say I have mastered that aspect of building yet. I have found one person at the city offices who is enthusiastic about answering my questions and finding the right forms/info, etc., so at least that's a start. I wouldn't expect to find a GC who would want to do your permitting for you, but you may luck out and find a bored, retired contractor or city employee with all the contacts you need to push things through, just keep shaking those trees.