What is the best 5k-plus Preamp with balanced outs and Phono stage?

Why not get an external phono stage? Rather than finish g a product that does both well, get two that do each excellent. 
 
The Bryston 17 cubed line preamp for those wanting brand prestige and looks, and the Benchmark LA4 for pure performance. 
 
The Parasound JC 3 Jr phono preamplifier would be excellent.

Have you looked at Backert Labs?  All their models have XLE.  A high-value sleeper brand.

Two great suggestions.
I was hoping I can find a high level preamp with a built-in phono stage due to space restrictions but if separates offer better value I'll make it work. 
I will look into your suggesstions

Check out Atma-Sphere preamps. They have balanced and phono!

http://www.atma-sphere.com/Products/

A second hand aesthetix Janus signature is what I have and enjoy very much.  An Atma-Sphere MP3 would be another to consider I would think though the Janus has more flexibility in terms of cartridges.

Audio Research SP-20.

How much over $5,000? for a little over, the EAR-Yoshino 868PL. For a lot over, the same company's 912.

Great feedback. I have my work cutout. 
I have no problem going a bit over. With all the options it comes down to system matching and value proposition. I learned that in many cases paying 10k versus 5k may not equate to 50% better sound. 

I second the EAR-Yoshino & AR SP-20. Also try to audition the Macintosh C2600 - it is a very capable tube preamp with an exceptional full feature phono stage and a warm yet detailed sound.

Going with separate phono stage might not necessarily offer better value due to costs of a separate chassis and power supply, but I would still suggest it because separating those will often give better sound quality. Better phono stages often have external power supplies to keep the low level signal away from the PS, reducing noise, more impactful with phono signals than higher line level signals. 

If we are casting votes, I love the Backert preamps, know the principals well, and can't say enough good things about their dedication to helping you get the best sound for your money. They are no nonsense guys with a professional musician doing most of their voicing/listening. They will spend hundred of hours comparing the sound of every damn capacitor, piece of wire, etc. to get the most out of their designs. The UI and clean design of their gear is appeal IMHO too, especially the top access to tubes, handy for tube rollers. Cheers,
Spencer

The EAR-Yoshino 868 is also available as a line-stage only. model designation 868L. Two pair balanced/XLR outputs (via transformers), two pair unbalanced outputs on RCA's, one pair tape outputs on RCA's. 17dB gain provided by a pair of 7DJ8 tubes.

I use an Atmasphere MP-3 with my Ayre MX-R (non twenty) with excellent results.
I'm still waiting for a non twenty KX-R to come on the market.
Bob

+1 on the Atma-Sphere MP-3

Be sure to add CJ ET-3 or 6SE to your list

ARC and Ayre always work well together, but you are getting great suggestions.....those are some incredible amplifiers....enjoy!!!!
VTL has some fantastic preamps now also, The Music Room a dealer here has a nice used model in your range, I believe it is a line stage...
no affiliation...

The recently discontinued Boulder 1010 would perfectly fit your description: an all balanced preamp with a very nice phono stage.

I operate a three tonearm turntable setup and also use the Boulder 1008 phono amp, which has two MM/MC inputs. You might think that the phono stage in the 1010 would have limited capabilities, thrown in as a bonus of sorts. But in direct comparison the MM stage of the 1010 is actually very close to the one in the 1008. However there is a huge quality jump using its MC stage, which for me justifies the cost. The 1008 has 70dB output and flexible loading, whereas the 1010 has 60dB MC output and a fixed 100 ohm loading, which doesn't sit too well with low output MC's. In order to accomodate those LOMC's I use its MM input with a SUT (vintage Entré ET-200 with 30dB output) to get the same gain level as with the 1008. In this configuration the sonics come pretty close to the 1008 in MC mode. Go figure!

If interested you should keeps tabs on hifishark for offers on the used market. The 1010 has been in production for more than 15 years, so they show up for sale on a regular basis. I think the going rate for a well preserved 1010 is around $6k. In my experience the Boulder is sonically quite neutral and not very fussy on the company it keeps (except its balanced only connectors do limit the choices). It's been a constant and highly dependable centre piece in my system that went through many changes over the years. I wouldn't know how it sounds with Ayre electronics, but at least they're both built in the same city!

BTW: the new Boulder 1110 has omitted the phono stage, so this is now a line stage preamp only.

I am looking for a preamp with a great phono stage to replace my Anthem D2V and match up with my Ayre MXR 20's.

Do you want the phono section balanced as well? FWIW all phono cartridges made are balanced sources (although they are not always treated that way by the tone arm wiring). To go with a balanced connection on the cartridge, usually all you do is replace the tone arm interconnect cable to the preamp. The advantage of this is that the cartridge is a very low impedance source, so the artifacts of the cable are thus minimized (since that is what the balanced line system is for anyway). This means that the tone arm cable does not have to be very pricey, it just has to be built right.

I was going to suggest the Boulder 1010 or 1012 (adds a four-input DAC), but user "edgewear" beat me to it.

Check out the Luxman Cl38U-SE. 

The most expensive one! LOL