This has all made my head spin. You have done a nice neat installation, but the speakers you have used are not designed to work that way.
If you are going to build a system in like that, then you have to have speakers that are designed to work that way.
The biggest problem I see is the subs, that are not going to produce accurate sound in that arrangement.
Those Klipsch speakers are not designed for that application either, as you have upset the full space half space transition. So I would imagine is has made them bass heavy.
For a system like that all the speakers need to be designed for such an application. Commercial speakers are not. It really comes down to the fact the speakers need to be custom. Even then you can reinforcement from the reflected wave from the wall at the lower frequencies which is hard to tame.
I have done a design and build for my wife and had hours of work into the design. It is designed to work in a wall from the ground up. It is a system we actually use a lot and my wife loves it.
You can see the
design approach, construction and measurements here. We have really enjoyed this system as well as the theater upstairs especially during this lock down.
You seem to posses excellent aesthetic design and constructional skills and look like an excellent candidate to learn to design and build unique systems.
The point is that having to use off the shelf equipment really limits the possibilities and performance of an endeavor such as yours.
