My setup is similar to shadyJ's initial suggestion, and I can confirm that the RX-V671 and VTF-2 are best in-class products. Below is a list of hardware that I run in my system, the prices that I paid including shipping, and where it was purchased. (everything was purchased in the last 8 months)
Custom built HTPC exporting audio via S/PDIF to DAC (~$700 - Amazon/Newegg)
DAC: Schiit Bifrost ($350 - Amazon)
AVR: Yamaha RX-V671 ($399 - Amazon)
Mains: Polk Monitor 70 ($320/pair - Newegg)
Center: Polk CS2 ($80 - Newegg)
Surrounds: Polk Monitor 60 ($220/pair - Newegg)
Rears: Polk Monitor 40 ($120/pair - Newegg)
Presence: Polk Monitor 30 ($80/pair - Newegg)
Subwoofer: Hsu Research VTF-2 MK4 ($589 - FD from Hsu)
shadyJ's suggestion of the Infinity Primus speaker line is a solid one, particularly considering Polk is phasing out the Monitor 30/40/50/60/70 series for the new 35/45/55/65/75 which is more expensive and has the exact same drivers. Another route I would seriously consider is one of Hsu's all inclusive packages like the Hybrid 2 5.1:http://www.hsuresearch.com/products/hybrid2pkg.html
If you really wanted to step it up and think long term, I would without hesitation recommend Ascend Acoustics' CMT-340SE speakers for mains/center, and their CBM-170 SE for surrounds. (having recently heard this setup, I wish I had gone this route myself)http://www.ascendacoustics.com/pages/products/speakers/spkrlist.html
As far as reliability between Yamaha and Onkyo AVR's, I'm really torn. My first AVR was an Onkyo that I used fairly hard for 3 years before it died. My second AVR was another Onkyo that I rode even harder and it's still running strong 7 years later. I've now had the Yamaha 671 for ~8 months, and it's running extremely well even though I occasionally listen at reference levels. On the other hand, my brother got a new Yamaha RX-V373 back in October, and he's already had the original, and then the replacement up and die on him. He's now waiting on his second warranty replacement. So at this point it's tough to say which brand is more reliable in my opinion. For what it's worth, Yamaha's warranty service is apparently easy to deal with, but fairly slow.
Best of luck with whatever you choose!