From what you have written, I think that a different rack system is what you should consider. Naim Fraim (or Lite) is one option - Isoblue is another popular choice. And as @Mike_S mentioned, you might also be able to swing an install into the deal…
Last time my system “Didn’t sound right” I thought it was all in my mind. It felt like it had gone off but I couldn’t put my finger on how. After a week or so I couldn’t let it go so I went through everything. Eventually I pulled the insulation off the soldered speaker cable connectors at the speaker end. One was broken and held in contact by the insulation only, another was connected by only two strands of the Nac A5. Over 10years of unplugging to clean the contacts they eventually failed. Obviously the original soldering left something to be desired. Not any more
The first thing you should do, if you haven’t already, is check the age and service history of all your Naim boxes, especially the power supplies and power amp. If they are old enough to need a recap (10 or 15 years) get it done, either by Naim (via an authorised dealer) or Class A in Sheffield.
Then get everything reassembled, ensuring that the basics of cable dressing have been observed, let it run for a few weeks, and see how it sounds.
Adding two Fraim stacks should help. It’s a substantial outlay, and if you buy these from a dealer they should be prepared to set them up for you. If they know what they are doing they should be able to get your system to sound as it should. I do think it’s worth approaching a few dealers to get a feel for what they are prepared to offer. Doing this while showing them that you might buy something from them, and not eBay, might help.
Just reiterating the importance of keeping power supplies away from sensitive components. I had a Lingo1 on the shelf below my old 250. If you moved the L1 slowly from one side to the other you could actually sense it moving through the speakers. Not a sound as such but a sense.
Looks like a SkyQ Mini box. If it gets as hot as my SkyQ Silver box then it should keep the room temperature about 0.5C above ambient. .
Seriously though, you can get 3d printed brackets for these on EBay for a few quid. If you are struggling to find somewhere else to put it. The bracket would allow either wall mounting or even on the underneath of the shelf above the PAs. Makes for a really neat install.
Looking at the third picture down, depending upon how much right hand bit of green wall there is, to the right, out of the picture, I would try and get some green wall behind each speaker and perhaps toe each of them in a bit.
The TV might have to be pulled a fraction to the left to do this. Obviously both speakers would come forward by 30cm or so.
I’d also swap the NDX2 and the 252 round to get the transformer in the NDX2 as far to the right as poss.
Speaker position looks not so good to me. Is this really the only possibility. Try also to have one input to the 252, I.e. the NDX2. Keep it simple for the start. Are you using the earth pin on the 252? Make sure 555PS, Supercap and 300PS are plugged into the same power block to ensure improved earthing. I would also try and dress cables to keep signal cables away from mains cables. Looks like you have power supplies to right and head units to the left which is good. As you found with your sky box keep interfering objects away as much as possible.
Agreed, the speaker positioning isn’t ideal. Appreciate it isn’t always possible in domestic environments to position speakers perfectly, but moving the speakers so a wall is behind as opposed to the side should help. At the moment, from the photograph it looks like one of the speakers is closer to the side wall than the other - I have found this to have a significant impact on sound and imaging. The furniture in front of the speakers won’t help this either.
Also, what speaker cables is the OP using? This can make a significant difference also. There are a number of affordable, and Naim compatible, options if currently cabling also isn’t ideal.
Much as I like the look of the Fraim In either form I would never invest in them. If it were me I would for now move the Sky box out of the way even if it means temporarily placing it on the floor somewhere. Then just listen to the music for a bit and see if this makes you smile. If so, keep the supports you have, there’s nothing wrong with them. You will eventually find a place for the Sky box that’s suits you and the sound, a bracket just gives more options.