Okay, good to know and you answered my question about using stock power cables (unshielded?). The only thing else left to ask about power cables would be that the gauge is 14 (AWG) for the Torus and amplifier?
As far as interconnects go, I'm not sure what the construction looks like of your Analysis Plus. Do you have any standard interconnects like Mogami 2549? I find that along with Grimm TPR are a good cheap solution to keep around as a reference. These are neutral sounding for me and have never had a problem with them tonally. I got them custom made for ~$20ish each. I did find one of my other more expensive interconnects a bit less suitable (Mogami 3173 and SCIN effect). I'm sure there's probably nothing wrong with your interconnects, but just throwing some ideas.
Maybe try readjusting the speakers (distance/toe-in)? You can put some masking tape around the spot where they are, so you can experiment and always have the option of returning back to the same starting point. If you have a headphone rig, that's also a great way to supplement and confirm whether what you're hearing on speakers is translating on headphones or not. You don't have to worry about the room at all.
If you have a picture of the room and/or the rack, that could be a good start. For example, I've moved the Torus and my Class D away from the rest of my gear, and to the side, rather than having them all vertically lined up in the same rack with all their toroids matching up.
Maybe take a look at the wiring again to see if it's a jungle back there or if the signal and power cables are stuck together? Simple plugging and replugging of all the cables to clean up the connectors. Just some ideas.