Hey, you're welcome

This does seem like a challenging setup!
For the living room (non-projection room) TV, I'm going to go ahead and strongly recommend that you track down either an LG 55LH90 or a Vizio XVT553SV. With the 45 degree swivel arm and the large windows, a matte-screen local-dimming LED-LCD is absolutely going to be your best choice. The lighter weight of the LCDs vs. a plasma is going to be a benefit on that swivel arm. And even though Panasonic has really improved their reflection/glare reduction and black level retention with this year's models, plasmas still use glass and there is only so much that coatings and filters can do!
It's such a shame that there are no current LCD models that offer matte screens anymore

But the LH90 and the XVT3 are both very good options. 55" is a little smaller than I would personally like for a 12-14 foot viewing distance. But then again, if you were going by SMPTE recommendations, at 12' you'd be looking at a 92" screen! So 55" is probably about as big as you can go in that swivel out location anyway
The LG LH90 offers more user picture adjustment options in its menus than the Vizio. As such, it's easier to dial in an accurate picture on the LG. But in a bright room, I doubt you'd notice the Vizio being slightly less accurate in color and grey scale. Plus, if you really want accuracy, the Vizio can still be nicely calibrated by a professional with ISF certification.
The LG has a HUGE border around the screen. I'm thinking that might be an issue with the cabinet and swivel placement. The LG also lacks any internet apps. So I'm thinking that the Vizio XVT553SV is probably going to be the better choice between the two for you
For speakers, I do think that Axiom is probably going to end up being your best choice in that room. You can certainly get their speakers in a white finish (with white grills, no less) for a very small upcharge. In a situation like yours where you will likely require less than ideal placement, I would recommend Axiom's M3v3 bookshelf speakers. The M3 are Axiom's most versatile speaker. They work well in almost any situation and they are available in a wide variety of mounting options including: regular bookshelf w/ an integrated mounting option for either a wall or ceiling mount (which Axiom also offers...and in white!), an on-wall version (although the mounting requires a flush mount on a flat wall surface), an in-wall version, and a cool in-wall/on-wall hybrid with a thin cabinet front and full backing box. There's even an outdoor version, which can also be easily mounted in almost any orientation.
If you're more or less forced to mount your speakers up in those ceiling rafters, I would recommend that you simply use M3v3 bookshelf speakers for all 5 or 7 channels. I'm not really a fan of Axiom's VP100 or VP150 center speakers. And Axiom's QS surround speakers work best with the intended side-wall, flush mount placement. M3s all around with Axiom's ceiling mount bracket would work best IMO and make your wiring job easier
Speaking of wiring, the best options I can think of are using flat, paintable wire, or just using those paintable "cable raceways". Neither will be invisible, but they'll be far less noticeable than just regular wire running all over the place

Axiom offers some over-priced flat wire. But I think your best bet is going to be Parts Express for flat wire options.
In the projector room, I'm going to stand by the Panasonic ST30 recommendation. The 3D is entirely an option: the ST30 models don't even come with any 3D glasses included! Panasonic's plasmas really are the best 2D televisions available right now, so don't get hung up on the fact that they HAPPEN to offer 3D as an option. You absolutely do NOT have to watch anything in 3D if you don't want to!
With the ST30, you can get a nice 60" or 65" screen size for that 12' viewing distance of yours
For the projection screen, I think you'll want to strongly consider an acoustically transparent electric roll-down screen. That way, you can still position your center speaker directly below your Panny plasma and then have the screen drop down in front of the plasma and center speaker without blocking the sound!
For a very reasonably priced screen, I have to recommend Elite Screens and their CineTension2 with AcousticPro1080 screen material. You won't find a better price on a tensioned, electric screen with acoustically transparent fabric!
I'm not as harsh on Onkyo as a lot of people. I've owned two Onkyo receivers that have worked for me without issue. But they DO tend to run hotter than most other brands and if you open them up, you'll find that they do tend to use lower quality, lower priced parts. This is an understandable cost-cutting measure, given than Onkyo clearly aims to compete on price and features. So they're not the greatest, but then again, they manage to undercut their competion on price and still sound good!
But in your case, you'll probably want to stick with Denon. I personally prefer Denon, Marantz and Onkyo for the simple reason that they offer Audyssey brand room correction, which I've found to be superior to Pioneer's MCACC or Yamaha's YPAO. In your room, it's likely that you'll need significant room correction. I would urge you to look for MultEQ XT level room correction. MultEQ XT32 would be nice, but that is still only offered in the top-level, higher priced models, I'm afraid. MultEQ XT is very capable though and should be right in your price range.
Blu-ray players can also be a bit of a crap shoot. I recommended LG because they tend to offer the most internet apps and streaming options, plus their players are very fast to load and they are very competitive on price. All manufacturers have to deal with the frequent updates, some are quicker about pushing them out than others. It's one of the biggest reasons why I favor a HTPC. Install AnyDVD HD and not only can you rip Blu-rays to your hard drive and watch them that way, but you'll always get fast updates from SlySoft so that you can just remove the stupid "copy protection" and menu restrictions!
Anywho, something that hasn't been covered yet are subwoofers. I'm guessing your wife would probably prefer subwoofers that are somewhat smaller than a fridge

Axiom's tiny EP400 is about as small as you can get while still digging down to 20Hz frequencies. The problem is that the little EP400 can only do it at rather quiet output levels, plus it's quite expensive! A better bet is probably going to be Rythmik, who offers some really nice, compact sealed subs. SVSound also offers some smaller, sealed subs now. The SB12-NSD is a great little performer in terms of output, extension and looks for the price.
Regardless of your subwoofer choice though, be sure to decouple it! I'm going to bet you'd love to be able to watch something in your theater without your wife being bothered by bass thumping away throughout the entire house! The reason bass seems to travel so much better than higher frequencies is because those long bass waves easily transfer into the physical structure of any building. They become structure-borne sound, rather than merely air-borne sound. When you subwoofer plays, it physically shakes. When it's sitting directly on the floor, the floor shakes too! The floor then shakes the walls, the walls shake the ceiling, and before you know it, you can hear that bass throughout the entire house and might even bother your neighbors.
Decoupling largely solves this common problem. I recommend Auralex' SubDude, GRAMMA and Great GRAMMA isolation risers. They're all the same thing, just different sizes. So get the one that fits your selected subwoofers. They'll be the best $50 you'll spend!
Finally, it seems as though your rooms are going to have acoustic issues for sure. So definitely check out GiK Acoustics to see if there is anything that will work - looks wise - in your room. Also check out acoustimac.com . They offer similar products at similar prices to GiK, but they have some more size and thickness options. Freestanding products like GiK's table and pedestal bass traps should also be high on your list. You mentioned that you still need to buy the furniture. I'm sure you need an end table or two! Why not make them a GiK bass trap table and get to "hide" your room treatments in the furniture budget
