Help! Advice and Recommendations please (system sounds bad)

Excellent system.  Some recommendations.  
 

1:  The mids seem muddled. Not rich…When the music is displaying a strong full spectrum I lose a lot of detail and separation.  These observations appear to me to be related to room acoustics, where there is cancellation and reinforcement modes muddling the mids and loosing detail and separation, especially at increased volume where the acoustic pressure may overload the room.  The recommended fix in the literature is speaker placement and absorption room treatments.  
2:  … getting some perceived distortion and harshness when the mids peak…This is more difficult. I think you indicate system was not in use for some months.  If you have not done so already, clean all contacts and treat them with the contact enhancer of your choice, and check all tubes.  If you moved to a more populated area, you may have increased mains noise or EM emissions.   You can have this measured or buy meters.  I do not see a power conditioner listed.  You may benefit from one.  Finally, if your previous location was a solid floor and now you are on a suspended floor, you may be experiencing effects of vibration feedback.  Decoupling your speakers may help.  

Good luck experimenting.   I am confident you will get back to the SQ you remember.  Ava in, excellent, well thought out system.  

Looked at your old room set up, it looked like it might sound great. I'm not so confident about your new room set up. I suspect that your issues might be helped by moving your speakers forward or backward to find the best balanced location so your bass response is smooth. Maybe involving moving your subs as well. In that respect I would probably set up my main speakers first without the subs and after I found their best location incorporate the subs. You may find totally different locations that will work well if not better.  Your photos make your set up seem a bit more congested (than your prior room). You might move your speakers a tad closer to the side walls (not such a big deal with panel speakers),and as rvpiano suggests, reduce their toe-in. I cannot tell from your photos but I assume you have your listening chair triangulated with your speakers. You might try moving your chair(?) backward and forward a bit. I note your present room is more problematic because of its dimensions. You might (if you can or if you haven't) consider firing them down the long dimension of the room. 

Good luck. :-)

Some of your deficiencies are symptomatic of speakers being hooked up out of phase. Just a thought.

@jordanmj 

The first thing that sticks out to me is the new wood paneling.  That can result in quite a bit of absorption vs the diffusers you use to have. Hence it will deaden the sound. And you need to liven it back up. Diffusers would be your best option. 

As to the servo Rythmick, I have a couple of those. Even so I have very different equipment as you can see under my house of stereo system, some of your sub settings seem off. I live next to Rythmick in Austin and know the owner. He has always recommended setting the volume to noon. Maybe down to eleven, but where you have it they would barely be in play imo. I also get best results with the low pass filter at 50 hz/24, extension freq 14 and damping high. Meaning we are quite a way off in our adjustments. Again different room and equipment will equal different settings, but just trying to help. Good luck.

Well if the problem is in both speakers then this narrows things down a great deal. I would think it is a room/acoustics problem. 

I have never experienced much or any absorption with wood paneling. My guess is the panel are reflective.