AudioBear: Nice setup.

Pythagore: You should probably lay off the tone controls for now, they're intended for after all the speakers are in balance. If your subwoofer has somehow become out of phase with your mains and they're fighting each other, for instance, increasing the bass tone control will just make them fight each other harder, and you'll still get a suckout that sounds terrible.

If you don't mind, what speaker trim values did you end up with after the auto setup? Maybe some of the other 990 owners can take a look at your numbers and see if something looks odd.