Looking to build a system for under $5k

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!

I suggest a used solid state amp to drive your Vandersteen speakers.  They are fine speakers and you can buy now if in a hurry.

for the amp, maybe a Hafler?

I also like the Oppo player for this - lots of used ones as people upgrade.  You may be able to get by with no pre-amp.  

Do NOT waste your money on any sort of expensive cables.

Also take a look at Cambridge Audio equipment; Rotel; and similar.

Marantz and Yamaha make good receivers if you decide to go that direction.

Try to save some money out for room treatments - much of which can be DIY - I've posted some links before on other threads.

One advantage is your room is non-square...

+3 for Vandersteen's. +2 for Johnny R at Audioconnection.
The Vandy 1's with subs can be a killer combo. Paired with a used McCormack amp and preamp, and a Schiit DAC. and some AudioQuest cables and you should be under $5K.
Though I am a Vandy fanboy, I really believe they aren't only the best deal for an accurate, listenable speaker, but also a good foundation upon which you can compare other speakers.
Bob

You got 5 grand to spend so don't let others do it for you.

And there are no components that offer a best bang for the buck.  If there were, that's all that would be available at a certain price point.  Everyone would want them and nothing else.  Instead there are hundreds to choose from.  So, there are only those components that work best with each other. 

Go to a few HiFi dealers and start auditioning speakers to find the pair that sounds best to you; not us. Vandersteens should be definitely be heard but whose to say your won't like them in favor of something else? If there are no dealers in your city, then day trip it to the nearest one that does.  Or plan on attending a 2 channel audio show. If your in the Midwest, Axpona is coming up in the Spring in Chicago.  In other words, take you time and do it right.

Don't be afraid to use half your budget for the speakers.  Build your system around these.  They are the only component you can actually hear and will be responsible for the final outcome from all sources.  Then look for an integrated amp that will properly drive those speakers.  Its ability to drive the speakers you have selected should be the first consideration in picking it out.  Everything will just be a feature like a phono stage or DAC.  These things can be added as external devices.

After speakers and integrated amp, then get your CD player with what's left.  Since you said vinyl would be down the road, then start saving all over again.  To do vinyl right will cost a lot more than a digital source.

Have fun and happy hunting!