nice! +t for the new home.
i can't speak for dedicated 2 channel systems, so i'll just suggest some HT options that would give you good 2 channel performance and good HT performance, especially with that nice 65" DLP.
if it was me, given that layout, I would go with a nice HT receiver in the living room. i would upgrade from the onkyo system, but you can cannibalize certain things for now. you could continue to use the surround speakers and the center channel and maybe even the sub.
how do the in-ceiling speakers work? i assume you need an external amp to power them, correct? in some ways, it's too bad that they have separate volume controls because the circuitry in that might not be all that great. if you went with a multi-zone amp, you could just power the ceiling speakers off that.
if you go with that 85" credenza, you could go with some nice bookshelf speakers and a better sub.
i'm looking at building a HT system for my dad, and i really like these b&w bookshelfs:
http://www.bwspeakers.com/index.cfm/fuseaction/products.models/label/Model%20XT2there aren't too many reviews out there but what i've seen are positive. I think they go for about $1k per pair. i think they look very cool, which you may or may not consider positive. but i would think the WAF would be pretty high.
that would leave about $1500 for receiver and sub. would you consider used gear or are you looking to buy new?
the new pioneer elite line has gotten good reviews, as well as your usual suspects from denon, yamaha, onkyo and maybe even used arcam stuff. (I'm waiting on a new arcam avr350).
like i said, if it was me, that's how i would go because i like to listen in the comfort of the living room. i know that i wouldn't enjoy hanging out in the loft just to do 2 channel listening that often. I fully recognize the limitations of going with a compromise 2 channel/HT setup, but unless your loaded, this stuff is all about compromises.
i'll chew on this a bit more, i've been looking into this stuff a lot lately.