First, the room. Bigger room or many openings requires bigger subwoofer. For your room, as long as you don't play extremely loud you should be able to get enough bass from $450 Hsu VTF-2 (in case you need more bass output compared to STF-2). I firmly believe that this little VTF-2 still can rattle quite a few things in your house.

Second, the receiver. If you are leaning toward Yamaha, I suggest to get 1400 and save the $ difference for speaker.

Third, Boston deal etc. It may be a good deal, but I'm afraid it's not a good start bacause you'll be stuck with it. Later if you want to upgrade you'll then lost $650. Not a good idea. The better start is to get a good pair of bookshelf speakers for fronts first. In case you want to upgrade, you can use them for surround. Forget about building 7.1 channel in your room. You don't have the place for speaker anyway. YPAO will help you to get good basic setup to optimise surround performance and you still can further tweak it if needed. Tilting down the front speakers at ceiling high as previously suggested may/should help creating lower sound image. As for surround speakers try to place them at various angle to achieve the best performance. My suggestion is place them facing to each other.

The last suggestion is be patient in building HT system. It's better to delay in 3-4 months to get everything rather than to get everything now and scrap them later. Good Luck!!