Upgrade path question with $2k to spend

first thing I would do is upgrade the phono stage. 

May I ask why you feel that way?  I mean my current Phonobox DS+ has multiple settings for MM/MC carts and seems like its adequate at $500.  If i upgraded to a $2,000 phono stage and kept my $500 TT and MC cart would that even make a difference?  My feelings were upgrading closer to the source.  

Your weak link is the Yamaha A/V receiver. Start shopping for a nice integrated amp. There is also nothing wrong with upgrading your TT, a good table is a point of pride and the center of your system. Spend way too much on it, you'll have it for a long time. 

@icegeek - I’m with @johnss - with the phono stage upgrade

I would recommend the Simaudio Moon 310LP - then you will be able to hear improvements of future analogue upgrades - you will hear improvemetns from your existing cartridge

Best Turntable Preamp | 310LP Phono Preamplifier | MOON - Simaudio

I have it’s predesessor the LP5.3 RS and I have stopped looking for a replacement

Prior to that I had owned several budget oriented phono stages and none of them came close to the performance of the MOON.

I did take home an LFD phono stage, but it was not a great match to my other components, so I exchanged it for the LP5.3 RS - and Voila!

The 110LP is also very good and it’s design is carried down from developments in higher models, so if you are uncomfortable with the 310LP price, then the 110LP is a great choice also.

You could then afford a cartridge from a company like Soundsmith

• I have the Soundsmith modified Denon DL103
• an excellent pairing with either the 110LP or 310 LP

I’ve changed cartridges a couple of times and the LP5.3 RS phono stage has revealed significant details with each uprade

The Simaudio products also respond very well when great cables are used with them. I recommend Zavfino, In-Akustik and Hijiri cables for best performance

Regards - Steve

If you are using the bult-in room correction, plug your main speaker's ports and run it again. :)

In general though, I have not heard Yamaha HT receivers in a very long time, but I do know that the quality of the sound processing, especially the DAC's of HT processors is really very wide.  The gap among products is really disappointingly wide, when you'd think it should be really close.  So, generally speaking, I would encourage you to try out an Anthem if you can find one, only because they sound good and relatively inexpensive.  For sure, not Onlyo or Emotiva.