Interesting thread. Super room mode calculator, NTK.
If I've gathered correctly, the bass cancellation has been entirely with regard to the main speakers, and no sub was involved (?)
But since the issue is is the 90 Hz zipcode, I'd like to think of the speakers as subs for a moment, and offer a few thoughts.
So here's a few ideas/thoughts that have helped me try to figure out rooms, and what's going on with bass.
In addition to room modes which I think of as independent of speaker/sub placement, I like to picture the idea of "virtual subs" .....which are created from mirror reflections with each and every room boundary that a sub's (presumably omni) radiation hits.
It helps me visualize 1/4 wave cancellations that occur between sub and 'virtual subs', and 1/2 wave reinforcements.
Helps separate one piece of the puzzle,..... is it a mode, or a reflection.
Another piece to remember is there will be 1/2 wave cancellations between two real subs, at every odd half cycle. (1/2, 3/2, 5/2 WL distance between ...for same signal)
A couple of 'sometimes hard to implement' measurement techniques:
The first is I make sure there's good summation between a single speaker and sub. If at all possible, i measure and do the xover work outdoors using the physical separation as planned indoors. Then I know once indoors, problems are either modes or reflections.
Hopefully the speaker and sub can be located within 1/4 WL of each other, for easier in-phase summation.
Not always possible though, or always desirable.
If subs can be located anywhere, another technique is the reciprocity principle...... put the sub in the listening position and move the mic around the room.
Which will show what the subs' frequency response will be at listening position, if it placed where the mic is.
Saves a lot of sub placement experimentation (if you can get the dang sub into the listening position Lol

)
If you have a real-time dual-channel transfer measurement setup, this test really gets nice. Even better, if it has automatic delay tracking (removing any constant delay & ToF in real time) you can quickly see what phase at listening position will be too..