$40,000: What 2-channel system would you build?

Well first of all it would have to be based on a turntable. Ideally the best used Teres Audio or Origin Live or maybe Sota I could get for around $5k, with the best arm preferably Origin Live and as much Koetsu as I could get new or used for around another $5k. In this price range the Herron VTPH2A is an absolute necessity, $3.6k, a little less than $5k so I would take the $1400 left over and put it into the arm or cartridge for a front end total $15k.

This will be very similar to but a little cheaper than my front end. 

Also in this price range the best value is probably gonna be the Tekton Moab. Efficient, easy to drive, with superb imaging, midrange and palpable presence. Its a little less but call it $5k. So 20 down, 20 to go.

Prima Luna integrated, stick with round numbers, call it $5k. For power, Perfect Path Technology The Gate, $5k. 

That leaves $10k for speaker cables, interconnect, 3 power cords, and a few essential odds and ends. Which is a little tight. But used Synergistic Research CTS speaker cables can be had for $3k or less, CTS interconnect about another $3k, leaving about a grand each for the three Synergistic Research power cords. Which you can get plenty good for that money, which will leave well over a grand for a few Blue Quantum Fuses, a few PHT and a set or three of ECT, however many we can get and still have enough to put BDR Cones under everything and two or three Synergistic Blue outlets to plug everything into.

I'm being generous with the above prices. With even a little price shopping you could still have a good $10k left over. In which case, in spite of the fact you said assume room treatment I assume nothing and would put about $2-3k into Synergistic HFT for the room and speakers.

That should still leave me with a couple to several grand for a good stand for the turntable. Not to be the least but the last $3k goes to four subs and two Dayton amps, for a killer distributed bass array that together with everything else makes for one super hot awesome fully fledged and tweaked music system.

@millercarbon  I like your thinking.  Thanks for sharing your thoughts, especially on the TT.  I know almost nothing about that, so thanks again.

I also really like you're more balanced spending approach.  I could be guilty of putting half in the speakers and then pinching a bit in other areas.    

I ascribe to the 'build-around-your-speakers'- thinking.  But many would agree that starting with the source is the best way. 

I definitely would like to get into a TT, but my vinyl collection is little and very old, and not sure how well it has aged.  (Navy storage while overseas and then when retired for another year)

Why the PrimaLuna?  If I'm honest, I'm leery.  I feel like Uncle Kevin is pushing that line so hard, it feels disingenuine.  What do you like about it, and how would you compare that to audio research reference?  Which, to me, can be had for a song on the used market.  I've had ARC, many pieces, and loved it. 

Thanks again. 

@erik_squires thanks for sharing. You've got one up on me; I've never even gone to an audio show yet.  Really need to.  How do you enjoy them?  Even if they are 'lower' end? 

Thanks all!

@erik_squires ,
+1
Though I have listened to only the Sabrina's-and found them to be quite good, Vandersteen easily beats Wilson not only in performance, but in price.
@OP, 
Likewise with Transparent cables. 
Though there is a case for 'synergy', I have to say that Transparent is way overpriced for what they offer.
Just my 2 cents...
BTW, is the $40K for new equipment, or used?
Bob

@gdnrbob  
Price can be either. I agree on the pricing of TA cables... but, I do like them. 
+ @erik_squires 
What do you both like about the Vanersteens? 

I've heard vandersteen, run by my Ref 75 (at the time). Treo or Quattro Carbon (CT)... I can't recall which, but it was about a year ago and current model.  I thought the sound was nice, a bit less fwd than I'm used to with Wilson and Focal.  I would say it was a nice sound one could listen to all day.  
I'm a little gun shy on the Vandersteen external cross-overs, dura-cell batteries, etc... Seems a little McGuyver to me.  But, can't argue w/ the sound and the price.  I liked the sound better than Sabrina, not as much as Sophia 3 or Sasha.  

Thanks!

@OP,
What you enjoy about a speaker is yours to enjoy.
Don't let me or anyone try to convince you otherwise.
What I will say is that dollar for dollar, in my estimation, Vandersteen exceeds whatever most manufacturers offer. And, though the external crossovers may not be the most elegant visually, they perform their functions in a most elegant way technically.

What do you both like about the Vanersteens?

I think your post answered your question...

 I would say it was a nice sound one could listen to all day.

I think that summarizes what I like about the Vandy's.
I tried a few set of Zu speakers, too. Thinking that a speaker without a crossover might offer a less compromised (electronically) sound (like you referred to 'McGuyver-ish'). They were very good, but lacking in a subtlety that is hard to put into words (think of Dr. Evil 😉).
When you pair Vandy's with either their amp, or Ayre or Atma Sphere, and use Audioquest cables, they really come into their own. (Zero feedback amps really seem to make them sing).
Bob