Auto, if you have a sub downstairs that isn't needed, why not move it upstairs?

I'm guessing in a huge room like that, it won't be overkill by any means, but might give you some lower end that you're not getting in that null....especially if you do the sub crawl to find the best location to fill the null.

If it works, then you can decide if you want the sub there, want a sub that might look more aesthetically pleasing in that nice room, or if you're willing to not use a sub at all.

But I would say that as long as you have a sub downstairs that's not needed there, why not try it upstairs?

If you didn't try swapping wires at the receiver, I'm still confused about how you tested for phase coherence (polarity consistency) among the front three speakers. Did you use a test disk or is there a Audyssey routine within the receiver or something?

And, yeah, just try a sub in there (in various positions) and see how that might work. That seems like less trouble than moving the M60's, and I think it probably gets you closer to your ultimate solution.

Have you tried adjusting the phase alignment or diverting some of the power from the main deflector to compensate?

I've had the same issue with my M80s; I've corrected it to a point where I don't think there is much else I can do. The system's low end sounds better but still not ideal (for me that is). From my listening position, if sit on the couch, it sounds like I'm into that bass null; if I stand up, I can hear a big difference in the low end. Weird.
In any case, what I had to do to improve the bass response was to move the speakers: distance from the wall, distance between the speakers and the toe-in. I played with this countless hours, but in the end it was worth it as I've some improvement for sure.
Now that you've read all this... you'll probably find it useless as I don't think it applies to your case?
In an effort to at least give you something useful, I would try a different set of interconnects (and I would've suggested speaker cables as well if not in-wall/cabinet speakers) and try a power amp.
One last thing: if you have your receiver plugged into a power bar/conditioner/surge protector, try switching it directly into a wall outlet; the reason I'm suggesting this is that I've heard with my own ears, where a power conditioner was taking the edge off an amp at louder volumes.