Building a system from scratch (other than speakers)

Thank you all for the advice so far. To clarify a little bit:

simao - I live in central Mississippi, so high-end audio stores and in-home demos don't really exist here. The company that sold me the Martin Logans went out of business. I do have an audio consultant that helped me with home theater but he only deals in Mcintosh and Rotel and has no inventory/sound room.

adg101 - I was trying to be all-in around $5K but can stretch that some I need to. 

mesch - honestly, I don't know what the partition will be. I have a fair amount of vinyl and far more cd's. I'm sure I will lean more towards one than the other after I build the system and have some time with it. I mostly listen to classic rock (think grateful dead to led zeppelin), some newer rock/alternative leaning towards more acoustic (think nirvana unplugged to dave matthews/tim reynolds), and some classical, jazz, and blues. Sorry I'm not more help on the partition, that's why I was leaning towards the relatively cheaper turntable. 

jafant - thank you! yes, will have to start a new thread for cable/cord recommendations when I get components figured out.

douglas_schroeder - yes, trying not to be hasty and finding that very difficult! I had an Emotiva xsp1 & xpa2 in my amazon cart the other day just because I was being impatient and wanted to get going - decided to try to be strong and seek professional help i.e. this forum. When you say server/mac mini, are you meaning storing some form of uncompressed audio there to play through the system?

pokey77 - I had no idea that ML forum site existed. Will drop in there as well and see what I can find. 

Thank you all very much for taking the time to give your input. I now have a lot of homework researching suggested components - that I'm really looking forward to. 

It strikes me that pretty much all of you are nearly if not totally encyclopedic (at least from my perspective) on this subject. How did you build up this knowledge base? Is it just building systems for so many years, hanging around good shops, or are you reading certain periodicals or review sites? I ask because I'm truly fascinated by hifi and have learned a lot from the research I've done to this point, but the amount of products and information out there just seems overwhelming.  

jafant - Actually the day before you recommended him I was researching Rogue Audio products and came across Wilson Audio. I called and told him I would be down Saturday the 13th to check out some gear. Your recommendation cemented it. Down I went and came back with most everything. Blew my budget a bit but think it was well worth it. 

marktomaras - I didn't even think of getting used cables. By the time I read your post I had already purchased. There's always next time!

The verdict: 
I went with the Chronus Magnum II with phono bypass mod. The other amp/preamps I liked but were just stretching my budget too much (which I still busted) were the Rogue separates (new), and a pairing of an (used) Audio Research hybrid preamp (blanking on exact model at the moment) and a Rogue amp from the mid 90's.
For turntable, I went with the Project expression carbon classic DC in mahogany.
For cd, I went with the Cambridge Audio Azur 35IIC. With this I bought a used California Audio Labs Sigma II DAC.
For a line conditioner, I went with a Furman Elite 15 PFI.
For cables I went with Audio Research SGL for speakers. Audio Research LitzLink interconnect (for CD), Audiostream interconnect (for phono), and an Aperture digital cable.
The only thing I am not terribly happy with is the cd player. Sound quality-wise, it is outstanding. With the Cal Labs tube DAC, it sounds very nearly as good as a used Audio Research tube CD player ($7500) they had in the shop. However, and perhaps you can help me with this, it has an audible tick when playing cd's. When the music is up you can't hear it but if the volume is down or when music lulls I can hear it from about 9 feet away in my chair. It is only when the cd is spinning. Is this normal, or is this a defect?
It sounds amazing. Thank you all so much for the help and input. 
I'd love you hear your opinions, especially on cables - as that is the only thing I didn't extensively research. 

marktomaras - thank you! I love the Rogue so far. A server or media player will certainly be in my future as budget allows. 

mesch - Yes, I will be contacting Wilson today. They aren't open on Mondays. The cd player will get me by until I can get some kind of media storage solution going.