I sympathize! I treated my room extensively prior to moving in based on nothing more than faith based on what I read in this and other forums. (Broadband bass traps on every wall juncture that I could, absorbers at first reflection points, and diffusion at second reflection points and on rear wall.)
I also used TrueRTA and Room EQ Wizzard pretty extensively. Played with locations of subs, phase between units, etc. etc. etc.
Easily spent over 100 hours on this.
Last weekend I had Jeff Meier of AccuCal (a professional audio and video calibration guy out of Houston) come to my home. He got far more done in that half day than I ever would have. He moved the subs around, we moved a small sub I had in another room into the theater, he moved the mains and toed them in differently, and then he dialed in some PEQ. The difference was staggering: far better imaging, tone much better, and far less boomy. (I learned a lot in the process.) It was, easily, worth the cash.
All a long winded way of saying, if you can swing the cash getting some professional assistance offers a lot of bang for the buck.