Well, I was really hoping that someone more experienced than myself (as I have no - ZERO - practical experience) would offer some ideas.
In the absence of that, let me give you some suggestions for what to try. Feel free to ignore me, or maybe my wrong-ness will at least spark some conversation.
My feeling is that one should start with the bass. The porous absorption that will be used (unless you are open to more advanced tools, that I can't really help with) will continue to suck high frequency energy out of the room. It would seem backwards to me to go about balancing reflected energy with direct energy and then go add a bunch of porous absorption messing it all up - so start with the bass so that you know how much of the reflected sound energy you've lost and can go about carefully adding it back (by either removing linacoustic and poly batting, adding thin reflective panels, or adding diffusors or some sort). Plus, if you've got an option to move subs, it's best to do it now, not later. Is that possible?
I don't recall exact built details, but I see in Morph1c's first post in the build thread he's indicated one sub behind the screen. It would seem that moving it side-to-side behind the screen would be easy. What about moving it out into the room or adding another? I'm looking at the decay times and seeing the ringing at 28Hz, which I would assume corresponds to a response peak (but we don't see a graph of the frequency response - can we get white or pink noise through the sub and see the response?) There's a similar hang-over around 50Hz. If these are troubling when listening to music, they would be the first thing I would look into. If they are a problem, I'd suggest (in order of decreasing effectiveness): adding more subs, moving the sub(s), a little EQ cut, a tuned bass absorber (or two), more bass traps. Of course, if the bass response is acceptable, we can move on to specular energy (above approximately 500Hz).
The psycho-acoustics I have read about say that you should not have high gain reflections at the mic within about 10-20 ms of the direct sound. Second, as you've noted, the room is somewhat dead. Given that, the goal should be redirecting or diffusing specular energy (in the horizontal plane as much as possible) without absorbing it. As you noted, the first high-gain reflection comes very soon after the direct energy (only 2 or 3 ms). If that's coming off the ceiling, then at least you've found it. Allow suggest a tilted panel that would reflect the sound to the back wall, over the heads of the listeners. If you have a spare sheet of plywood, maybe you can rig up a way for it to hang down in front of the screen at an angle? Here's a visual reference:
To go along with the "quiet time" following the direct sound from the speaker, at least in a two-channel environment, listeners often like a "kicker" to clearly define the end of that period. (I couldn't tell you why, or if it will translate well to home theater, but that's the only frame of reference that ever gets discussed and cited around here) So, if you want a kicker, where do you generate the high-gain reflection that will produce that psycho-acoustic effect? A little math - sound travels approximately 1.13 ft in each ms. For the reflected energy to arrive at least 10ms after the direct energy, the path it travels must be at least (10ms divided by 1.13ft/ms equals 8.8ft) 9 feet longer than the direct sound. In order for the reflected sound to be of adequate gain, it will need to come from a large area. The large central area of the rear wall is probably adequate size. If it's 4.5 feet from the rear rows ears, I'd say it's a good candidate. All that is to say: try it again with no linacoustuc on the rear wall and see if that helps.
And naturally, as a general statement, it's tough for anyone to know with any confidence what changes in a graph are going to be audible with real content. At every step, listen to some real sounds for reference. Maybe pick the first three minutes of The Dark Knight and watch it over and over - it's got good bass, surround effects and dialog so that you can compare.
Now that I've vomited that into the thread, I hope it's useful.