Looking to build a system for under $5k

See these reviews about Schiit Audio components.  In particular note the reviewers comments at the end of the Ygg review.  
(i.e., Ygg>>Rag>>KEF LS50).  

Maybe think Oppo universal player in place of the Ygg to save some bucks.  Used will definitely save you bucks if you can find something that won't need immediate maintenance/repair.

Do try and get out to hear as much gear as you can - "educate your ear", as it were.  

Also, look at some of the budget systems here under Explore (Explore>Virtual Systems>Tags>Budget Minded).

Good luck in your hunt.  Lots of good combinations out there.

Ragnarok review
http://www.stereophile.com/content/schiit-audio-ragnarok-integrated-amplifier#jgGoqy06UZcgAjix.97

Yggdrasil review 
http://www.stereophile.com/content/schiit-audio-yggdrasil-da-processor#su5mQISbEdAHtZRq.97

Good advice to audition some Vandersteens or other speakers first. Then choose an amp that is a good match for your speakers; proper power rating, features, and tonal characteristics that are right for your taste.
An integrated amp would be the way to go to fit your budget. Some integrateds have a phonostage built-in for a TT/cartridge, or you can use a dedicated phono preamp.

Thanks so much! Audio Connection is already on my radar as a source to check out!

You may want to prepare for the future, (which is music streaming), by looking at an Oppo spinner which plays CD’s and can accept streaming services.

In general, I'd advise thinking about the long term. Ask: will I always be in the upstairs room with smallish dimensions? This might change your approach somewhat.

For what you describe, I'd go this way. Prices are approximate, presuming you'd shop around some for slightly used/demo stuff:

-Rogue Sphinx integrated w. phono stage: $1200.00
-Sony HAP-Z1ES digital server (you'll stop using CDs forever, and you'll be able to stream Spotify too): $1800.00 (or less)
-Vandersteen speakers that you mentioned: $750.00 (?), because you like them. Or get smaller monitors (ELAC?), many possibilities for <$1000.00
-Hsu Research Subwoofer (various models available): $500.00. Subwoofer is the best way to get real bass in a small room.
-Use the stock power cords for now.  Upgrade them later or not.  Use the rest of your budget for inexpensive interconnects and some speaker cables.

good luck!