3. I'm also in the process of building a DIY NAS and started with Ubuntu Server. However I got really bored with just using the terminal. I'd recommend just installing Ubuntu Desktop for ease of configuration. In all likelyhood the performance impact of using a "heavy" UI OS is going to minimal when your requirement is to serve files over a LAN, WAN and do a bit of torrenting.
4. I actually went for an i3 purely because it had the horsepower when it needs it but can idle better than the Atom. I can't be arsed finding the article that showed this.
If you aren't needing RAID > 2TB I'd suggest picking up a ReadyNAS Duo. This is the only reason I'm building a DIY NAS. It does everything I needed it to do and it will do everything you listed. Just pick up the unpopulated version and whack in your own drives. It's add on's are pretty good and the Transmission web client is the biz.