Let me begin by saying this is just my opinion...
1. The 5803 receivers are complete and total overkill for the smaller rooms. The speakers (which I have not heard and can not comment on for quality) are small and do not need nearly what the 5803 can put out. Not that the 5803 isn't nice, but it is wasted money. That money can (and should) be used elsewhere.
...like...
2. For the budget that is there - that is a piece of junk projector. Unless there is no care at all for the video quality in the theater, the Cineza is at best, an average LCD projector when compared to the Panasonic AE-700 or others. For some reason people will spend thousands of dollars for a small improvement in audio quality, then think that a $10,000 projector isn't better than a $2,000 projector. Look at the Sim2 HT-300 projector or the new Sharp 12000 or Marantz S4 DLP projectors. Or go all out with a 3 chip DLP... which is the best way to go for sure if budget allows.
3. I have not seen a single 'in-wall' rack system that has been convenient or as reliable to service as any floor standing, permanent rack with rear access. Find an equipment room, face a rack into a room with rear access from another location, do not put a rack in any room with video where it matters as it generates a lot of heat and a fair amount of noise and light which is distracting... Best option, is a small room with decent ventilation that you can get to the back of the rack, then just set the rack on the floor. Oh, and make sure you have enough rack space before you try to put a dozen individual Niles amps in there.
4. Speaking of Niles... You know you are doing distributed audio, so why not a single 12 channel @ 60 watts (or 30 for that matter) rack mount amp? Niles has their 1260, Sonance has an incredible 1250 - Crestron has an incredible (and pricey) 16 channel... Multple amps just end up taking up room, and I have not ever heard one that sounds better than a multi-channel distriubtion amp.
5. Don't know about the projection screen... always gotta take a long hard look at Stewart Filmscreens though.
6. Hope Polk is giving you great pricing or it is a customer request - that's a lot of one brand of speaker.
7. Not a ton of additional work needed for control side, but I wouldn't use the MX-3000 in any room - ever. The Harmony remotes will give much better control than that will and neither will be as user friendly as a TPMC-10 in the family room that is similar to the one in the theater.
