Upgrade path question with $2k to spend

Replace Yamaha with Parasound Hint 6 int. amp.

I, too, have a blended system, but my AVR is an older Denon AVR-X4000 (which was their flagship AVR at the time).  The important thing is that your Yamaha appears to have pre-outs.  I run my Denon pre-outs through a Parasound P5 preamp then to a B&K EX-442 Sonata amplifier to power my Maggie MMG mains.  My surround speakers (Elac Debut 2.0 B6.2) come off the P5 and run through an Adcom GFA 6000 5-channel amp (nothing else is connected to it but those two surround speakers).  I don't use the internal Denon amps for ANYTHING - I don't run a center channel speaker.  Denons run famously hot already, and mine still does, even with all the power handling offloaded to two separate amps.  If you don't need surround speakers, great.  You probably don't even need a separate preamp, but I wanted one strictly for two channel music (or 2.2, as it currently stands).  I'd say that, from my angle, one of the easiest ways to improve your sound is to get your mains off the Yamaha AVR receiver and feed them from a separate amplifier.  That would be my first move.  If you don't want to add another component (which certainly makes sense ) then the alternative is to do as suggested:  get an integrated with a HT bypass.  The key to these blended systems (and getting them to sound their best for their respective applications) is to have a preamp somewhere in the chain with a HT bypass.  Gotta have it, IMO, to carve out as much of the "video" signal path from the music signal path.

Luck.

Hey Icegeek, I will bet your rig sounds good. It reminds me of a rig I put together. Many have suggested changing out your Yamaha. I’ll also had a multi thousand dollar Yamaha processor with direct mode and all the other bells and whistles. I upgraded cart, phono pre, speakers. When I finally went for a modest Odyssey Cyclops the sound was so much better. So that’s my story and what made the most noticeable and rewarding difference. Everything prior to that was an improvement but not that big a deal. The amp is the heart of it. Get that sorted would be my suggestion. Everything else looks great. 

you need a bonafide 2 channel amplifier as the foundation for your system before you do anything else, or you will not get the most out of any other upgrades.  

A musical fidelity m5si will do quite nicely

What do you feel is the 'weak link' in your system based on how you use it?

Upgrading the Rega P6 will be a significant upgrade - my initial concern is you won't be able to realize the difference with the home theatre receiver.  The change in materials on the table and the better cartridge are very discernable in a revealing system.

I'm not familiar with your specific units; I experienced a significant upgrade when I transitioned from home theatre receiver to an integrated amplifier.  Going source first provides future value if you upgrade the pre-amp/amp down the road with equipment more revealing than your HT amp.