I love blueprints.
I have only a couple suggestions.
First, if you have not already done so, peruse the Axiom Custom Finish Shop
and Custom Wood Studio
. I can't believe there isn't something in there that wouldn't please your wife.
Second, that subwoofer thing has me worried. I think you need to budget enough money to ensure getting a high-quality finish on your sub (whether it be Axiom, Hsu or SVS) so that you can have it out in the room, serving as an end table. That's a big room; I'd get at least a mid-level sub rather than anything smaller.
Finally, I don't have a good vision about how the plasma and the speakers will be put together in your custom built-in. If it were me (I wish) I'd be looking for some kind of wall mount for the TV - perhaps with a telescoping action - so that it doesn't end up being at the back end of a cabinet box (otherwise, those people sitting on the side could have a problem with sightlines). If you can get a dark, matte finish directly behind the TV, that would be good (I know I'm dreaming...). If your carpenter could rig up some sliding shelves for the speakers to sit on, perhaps you could pull them out of the "cabinet" for critical listening and slide them back in for times when viewers care a bit less. I'll bet you could tame most of the cabinet effects that way.
You should definitely call Axiom about the finishes; I understand they will send you samples for a small fee which is then applied to your purchase.
I think the M60's are great - I really like mine. However, given that you will continue to have a dedicated two channel system in another room, I'd get the M22 and a better sub in this room rather than the M60 and a less-capable sub. Blasphemy, I know.