This where the room eq knob on the MP2 is very useful, intended to adjust between very bright (shiny wood, glass) and dead carpeted rooms. Works quite well so similar eq is an option.
The cabs will definitely couple the way they're stacked, particularly bottom end. A bit more space between the 2 stacks will help a bit. Up off the floor is the go, but you've done that.
My other thought is standing waves which are always prevalent when you have parallel surfaces (e.g. walls/ceilings/floors) and why studio control rooms have angled walls and glass (and big active bass traps, generally along the back wall). A good way to visualise what standing waves do is from the beach when a wave going back out to sea collides with a wave coming in, makes a big splash typically up and down (you get to see the up), thus standing wave. The longer lower wavelengths (bass) are more prone (so bottom end rumble/mud) as those frequencies double in power from the collision. So not aiming your cabs at the opposite wall will help as will hanging thick carpet/drapes 3 to 4 inches in front of the wall, they need to be able to move so hang them, some of the bottom end will be absorbed (turned into motion of carpet/drape). This is a crude active trap. You can do more targeted sophisticated bass traps, simple design is long rectangular box with absorbing bats/rock wool whatever, hanging down vertically from the top inside the box and the box entry point (e.g. 12" square hole at front of one end of the box) for the bass to go in, bats turn it into motion so trapped. The size of the entry is tuned to various frequencies by its size (though not so critical with porous trap). Look up active traps (http://en.wikipedia.org/wiki/Bass_trap), what I've described is a porous bass trap.