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OP, you mentioned you have a budget for an upgrade. I have been holding off for a new thread but may as well get started. I don’t see a weak link in any of your components. Paradigm/Lyngdorf/Anthem/PS Audio is all top shelf.

Is there a problem in:

A) Component synergy/mismatches?

B) Room/system interaction?

C) You are a tough customer? After being around studios and studio budgets I would get that.

From your pics my guess is room/system interaction but IDK for sure.

@Kota1 Lots of great points one very striking one that goes right along with the OP is speaker cables. If they are a component and worth the price many people are willing to pay then eliminate them and go with active speakers. Many people who have decades of experience in listening to sound systems do think speaker cables do make a difference ok then why not listen to them and eliminate the cables we then that forces class D amps, Peter Lyngdorf has a speaker test with his D amps, you turn up the amp to 100% you put your ear next to the speaker driver if you can hear it buzz you don't have to pay for the system, 137db dynamic range is extraordinary in Steinway Lyngdorf systems. P Lyngdorf is a walking vault of patents for class D amps and his equipment may be an exception but it does mean that class D amps and 3.2kw power supplies are for real. 

OK, you got a Lyngdorf processor and PS Audio amps, the toobs are high maintenance and nickel and diming you on replacements.

Lyngdorf amps are of the two channel variety (SDA-2400) and at $2400 that works out to $1200 a channel. Your atmos rig has 11 channels so is it worth $1200 x 11 channels= $13,000+ to add 6 of those amps to your stack and hit the bid on the toobs?

If you miss your toobs get a tube based headphone amp. This one has a preamp out so you could use it as a 2 ch preamp as well.

You could hook the RCA out from the Manley to the RCA in of the SDA 2400 and the XLR out of your processor to the XLR in of the SDA 2400. You can switch between the inputs on the back and that amp would be driving your Paradigm 9H's.

@kota1 I've got the worlds most analytical headphone setup, the Focal Stella closed headphones and a Naim Unity HP headphone amp, both components are razor sharp and not very fun to listen to, accurate ya probably very much, I got that for working on video editing when you rally have to get the tiny details. Tube amps for the headphones would be great, I met Mr. Manley once he was very nice and very proud of his tubes and the way they sounded. 

I now I want to be active on my new system but I can't find a company that is totally system oriented other than Steinway and just 2 channels are $166K, and they don't even make surround speakers and I can't integrate the Steinway system into anything the connections are completely proprietary using cat 5 cable. I do want to put my money where I feel that the science and common sense leads but there are no alternatives. Sad.

I can't find a company that is totally system oriented other than Steinway 

Have you ever auditioned a system by Meridian?

I do want to put my money where I feel that the science and common sense leads 

Example of a common sense room, based on Meridian tech: