I would consider something like the Denon X4100W (or one of it's more powerful brothers).
The reason for this model (and higher level ones like it) is that it allows you to configure the sound set-up by source. Thus, if you are listening to your Phono or CD player, you can have it automatically go into Pure Direct mode in stereo. When you select DVD as your source, you can stick with the regular HT settings. It just automatically remembers your configuration for four sources which you assign via "quick buttons" on the remote. I think it is pretty slick not to have to reconfigure anything when you go from Phono to DVD and back.
http://www.accessories4less.com/mak...atmos-receiver-wi-fi/bluetooth/airplay/1.html
I don't understand how you are hooking an integrated amp into this system, could you elaborate?
If I understand your objectives, I would generally think in terms of having the main (L & R) signals directed out through the pre-outs of the AVR and into a separate power amp.
So for stereo, you can have Pure Direct (all processing by the AVR is shut off to avoid any chance of interference) feeding into a separate amp. That is about as clean as it gets!
For HT, you will have DTS (or whatever format the disc suggests), with the mains still powered by the external amp and the surrounds and center fed by the AVR's amplifiers.
The AVR I linked costs $650, leaving $850 for stereo amplification.
I'd probably go with Emotiva XPA-100 monoblocks for $640 a pair just because I like the idea of monoblocks, but the XPA-2 is probably a better deal at $720 and may be a better alternative if your speakers need lots of power.
https://emotiva.com/products/amplifiers/xpa-100
https://emotiva.com/products/amplifiers/xpa-2