As far as sound quality goes, might look up some posts by Audioengr, I think he mods Transits to improve the clock, and I gather Transits take modding well. I personally dislike toslink, so you might get him to install a coax output instead too. ;)
Personally, I use a Waveterminal U24 USB audio device, but I gather from another thread that they discontinued them. :(
As far as the other parts, many will recommend foobar as a great player, and indeed it is. Unfortunately, foobar doesn't like Apple Lossless and I find the interface a bit non-intuitive. Apple does great UIs, so I'm sticking with iTunes.