Thank you for all your help.
I've done some listening tests now and 90hz crossover unfortunately introduces too much bass localization. It feels like the bass does not fill the left side of the room. 80hz and below that is gone.
So what I did was set it to 80hz and play with the sub dsp and phase to get the MLP as the best, and at the same time monitor the other 2 listening points and make sure I'm not completely destroying them.
I ran the sub a bit hotter. It is now 7dB hot. I also enabled Dynamic EQ, but set the reference to 5dB, otherwise at lower volumes there is too little perceived bass. I think something to do with how the ear hears it. But at 0dB it is way overboosted. At 5dB I get no additional bass boost at louder volumes (verified by REW), where the movie listening usually is (-10 to -8 dB for DTS and -6 to -3 dB for Dolby). The optimal phase was 30 degrees (I tried 5 degrees at a time).
I also set the Audyssey setting to "reference" instead of "flat". It introduces a little bit of top end rolloff. Barely noticeable, but it makes the soundstage warmer. The mid-range comp I also turned off, I like the highs better with mid-range comp off.
Here is the final sweep at the MLP with the amp set to -8dB. I don't think I will ever run out of headroom on the bass on this sub. This subwoofer does 113 dB without distortion and I will never ever listen even close to that level in this small of a room, it's way too loud. 100-105 dB will probably be the highest I will ever go to.
I did do some tests at different volume levels and everything looks good, the whole line just goes up and down (well, until the Dynamic EQ is enabled, that boosts bass at low volumes).
View attachment 1475763
Before I changed the sub and corrected it:
View attachment 1475771
All in all, if I compare to what I had before:
1. The bass sounds massively better now.
2. I don't run out of headroom on the sub and don't heat the voice coil (although the PB2000 Pro is clearly overkill for my room, but the PB1000 was a little underpowered, I think PB 1000 Pro might have been the ticket).
3. I have learned a great many things over the past of few days.
To those that contributed, especially Conrad - THANK YOU!