I saw your original post a couple weeks ago, and I thought, "this looks like a pretty solid living room setup. You've thought through the dual screen and multiple uses. I don't know anything about your equipment, so I'll keep my mouth shut."
Now that you're having some glitches, maybe my perspective is more useful, so here's some thoughts.
Is the vertical placement problem because of the fan? Depending on your budget and ingenuity, you may be able to use an adjustable mount of some kind (powered lift) so that the projector can be close to the ceiling when you're not using it. Also, investigate the vertical lens shift feature; by shifting the image down on the wall, you may be able to clear the fan (if that's the problem). In fact, you will probably enjoy watching the screen lower anyway.
Unfortunately, I don't think lewke's suggestion to mount the projector off to the side will be useful, since the projector only has 25% horizontal lens shift. If you were to place the projector like lewke did in his attached picture, you'd need to aim the projector at the screen to get the image on it, but then the projector would not be aligned correctly. Whenever the projector is not totally "normal" (that is perpendicular in all planes - both horizontal and vertical) to the screen, some sort of optical distortion will occur - generally the image comes out shaped like a trapezoid, not a rectangle. Most projectors have a keystone correction feature designed to correct this, but the image manipulation that goes on degrades the image and should be avoided at almost all costs. Try it and see.
So what other options might there be? Well the projector is generally table-top mountable. You may need to invert the image and adjust the vertical lens shift, but it can work from some place near the chair, but that will be inconvenient. You probably won't want to leave the projector out in the middle of the room all the time, for both aesthetic and practical reasons. Without exact dimensions other solutions are more difficult to predict, but you may be able to wall mount (shelf mount near the wall?) the projector near the door and dining table, depending on the length of the room and your image size. In some cases a vertical compression anamorphic lens can be used both to get a cinemascope screen ratio and simultaneously lengthen the throw. (check out the CIH - constant image height - subforum)
Now back to your original concern - the acoustics. You can expect that your space, if decorated as shown and constructed of masonry, will be excessively "live" and suffer some acoustic problems, like flutter echo, and maybe some very strong early reflections that will interfere with your hearing sounds clearly. There are a couple common areas of wall that reflect sound in troubling ways. The walls directly adjacent to the speakers (directly behind them on the front wall, and on the side wall near each speaker) will reflect sound that will interfere with the sound at your seating positions changing the frequency response. These problems can be largely avoided by applying sound absorbing material on those sections of wall. Zammy's suggestion of OC703 is pretty good.
In my opinion, the best thing you can do is to start with controlled directivity speakers
, and toe them in. Then treat the wall under the TV so that the sound field is more symmetrical. If you have flutter echo, I would recommend continuing the treatments above the sofa and above/around the TV.
But hey, what do I know? I'm just some dude on the internet, right?