How big is a 90x103x51 screen? Which dimension is depth?
I guess you mean 90x51 or 103 diagonal. I guess you mentioned an acoustically transparent screen so you can go for in-walls, to keep the speakers from covering the screen? Our theater is 18x10.5 and we put in a 100x56.5 or 114.5 diagonal screen:http://www.avsforum.com/avs-vb/showthread.php?t=883876
Yes, from the side seats the speakers just barely clip the screen, even with the speakers closer to the side walls than I would like. Fact is, mostly there will only be 2-4 people in the room, so the "bad" seats won't see much use. Just put people there you don't like.
Anyway, your room is 6" wider than mine and your screen is smaller so I think you can use floorstanders if you want.
Your specific questions:
1) You kind of answered your own question but... Orient it like you have it, so you can put the equipment behind the seating in the alcove. If you can't fit the equipment there because of the furnace, then rotate it 180 so you are furthest away from the noisy furnace. You probably can't eliminate all sound from it. In this case, you can put the equipment next to the back row, like I have done.
2) We had a hot water heater right in the theater. The solution was to just disable it while the theater is in use with Insteon. Make sure if you cover it that the furnace can still pull in fresh air.
3) Calculate the depth of the back row seating, leave some space for people to walk in front of the seating (I left ~24"), then figure where the head's of people in the front row are. The rule is sit the people 1.5 times the screen width from the screen to their head. So figure the distance between the front row's head and the screen, then multiple by 0.6666666 (1/1.5). This is the screen width. As mentioned, the only reason you'd use an acoustically transparent screen (in your room) is to use in-walls. BTW, with two rows you will need a riser.
4) Directly behind is best, but below is usually easier. You just want dialog to be coming from the screen. Most mounts tilt the speaker slightly toward the listeners' heads, eg:http://www.standsandmounts.com/index...OD&ProdID=5544
5) What projector throw problem? Does the PJ you want not have enough lense shift? That doesn't sound right.
6) In my 10.5'W room, the surrounds for 5.1 are very close to two of the seats (the same "bad" seats already mentioned
). I could put two more surrounds on the back wall, but I don't think it is really necessary. So yes, I think you can do 7.1 if you wanted, just remember that some seats will be too close to the surrounds.