The Harman-Kardon 3490 stereo receiver would be perfect for you if you want to run a 2.1 system and are trying to stay under $600.

It has subwoofer outputs and plenty of power, with very good sound quality (much better than any Yamaha). You should look at its manual online to see for sure about the connectivity and control for your setup, but I think it may have what you need. It has several audio/video inputs that are switchable, plus a digital input and phono input.

If someone did want 5.1 for movies, then the Harman-Kardon AVR 1700 is what I would suggest. It is also fairly good.

You should be able to get either one for well under $400.

I have an extremely negative opinion of the sound quality of your Yamaha AVR, and my advice is to sell it for a few bucks and good riddance. You have great speakers and a good turntable, but that receiver is a problem. Either one of the HK receivers should be a very significant sonic improvement IMO.

To get an AVR that truly has high-fidelity sound quality, you would need to buy a Cambridge Audio AVR, which has excellent sound quality; far better sound quality than any other AVR I know of. They start at $1200, however.

That HK3490 is an awesome receiver for the money but last I looked, it doesn't have and HDMI input.  Check the specs before you buy it if that is a critical need. 

I you want all of those units to be connected, I believe you will need and AVR.  I haven't listened the the HK1700 but if it sounds anything like the 3490, you will be very pleased.  You can get some good souning devices from Denon and Marantz and they are probably worth demoing especially in that $500 to $700 price range.  They won't be in the same class as the Cambridge, unless you spend more ($1500 -$2000).  I have a 2 or 3 year old Denon AVR 1912 which I bought for features you don't need (Airplay & Pandora) and have been pleaseantly surprised with the quality of the sound for the money spent at ~$475.  I know it was replaced by an AVR 1913 and may have since been replaced again.  It is a good value and has a nice iPhone ap that can be used as a remote. 

They are not very conservative in the stated power rating.  50w per channel from Marantz is not going to be a lot of power.  That 1604 is a feature packed device, and I am sure it will sound great but I would be wary of pairing with those Wharfedale speakers.  If you were pairing it with some Klipsch speakers that are super efficient, I would encourage you to go with the Marantz. 

I think you will be wanting for power even if you don't listen with a lot of volume.  Given those speakers, I would probably not consider anything below the SR5008 in Marantz's line (which is $899). 

That HK1710 looks like a great value and should give you the power that you need.  I personally have not heard it. 

The best thing you can do is go demo a few systems.   Alternativey, purchase from someone with a very liberal return policy.  I would demo Denon since it is a similar sound to Marantz (same owndership - D&M) but carries a cheaper price tag on comparable equipment.  Onkyo as it tends to be a good value and the HK receiver you are looking at.  I don't like Pioneer and Sony personally and I find Yamaha to be too bright but my opinion is worth what you paid for it.  If you like it, that is all that really matters. 

Best case is that you can listen to a few devices and find one you like that in your price range.  Take your own music if you can and if you can go to a dealer that has Wharfedale speakers, even better.  It won't sound the same as in your home, but its better than buying based on reviews.