There’s a lot going on here. As stated you have quite a few room, reflections in the measurements, but if you want to keep those, I would start by figuring out your z-offsets. I can’t tell if you have figured that in or not.
This shows you how to do it all in xsim.
Once you have figured that out, we can go to step 2.
P.S. If the bottom woofers are going to play the same frequency range, you might as well measure them together.