OK, so if I understand you need a DAC, integrated amp, headphone amp, and a set of bookshelfs? For $1000...
OK, heres what I am thinking, I may be way off with what you are trying to do...
https://emotiva.com/products/dacs/xda-2 this dac is awesome I own 2 of them, and the headphone amp that is built in ROCKS, I have used many internal headphone amps {parasound, yamaha, little bear, Fostex, valhalla, and a few others} I actually own a fosgate signature tube style {these are around $1500, I traded a set of tad monitors for it and some money} and don't pay extra for the vanity, you will like the sound of the internal unit in the emo better, I know I do...
Next for an amp you may as well stay with emo
https://emotiva.com/products/amplifiers/upa-200
and that leaves enough for a set of these bookshelfs
http://www.musicdirect.com/p-76596-epos-epic-2-bookshelf-speakers-cherry-demo.aspx
that will put you at $870 so if you really just had to have a headphone amp you can get one of the cheaper little dots, or call emotiva and buy a bstock xda2 and a bstock amp you will save another $75 or so...
epos not on demo for $50 more, I would buy the demos ...
EPOS EPIC 2 BOOKSHELF SPEAKERS (PR) at Music Direct
there are many bookshelfs out there that sound good.. the Epos are a nice warm bookshelf, I don't think for a critical music system there is a better deal around anywhere rite now..
Classic Two (Black) B-Stock| Bookshelf Speakers | Premium Audio Equipment
a sub would make it even better, you can their 2.1 for $499 with supers, or $599 with 1's both come with their 8" sub that isnt super impressive to me, but the 2 linked above sound nice..
there are tons of choices in bookshelf speakers, you just kind of have to listen to them all..