Total bass suck out at 40hz

Is the test tone playing at 40hz or is it a dead track? Try another speaker.

If the file is good, then check to see if your woofer is moving at 40 hz. 
This is why I always measure frequency decades one foot from each speaker before I measure at the listening position.

Wow lots of really good stuff.
before you ran your test did you notice anything wrong. I believe its
a null in your speaker crossovers.
or room acoustics, your speaker cables play a big part in your system as well. I doubt your speakers will reach 20hz nor would you hear it. But you should feel it, 
Even if you move them around you’ll lose some else. Do you use a line conditioner? Do you use an equalizer ?Many factors come into play, Put all your test equipment away, and use the best test equipment there is, your ears. Enjoy your music! GT
alien tweek audio

The only frequency response chart I could find for the NS-1000M inexplicably stopped at 200 Hz, but according to that chart the NS-1000M starts to roll off at approximately 630 Hz with 200 Hz being approximately 6db lower. According to Hifi News test figures 53 Hz is another 6db down from 200 Hz which leads me to believe that 40 Hz is rolled off even further.

The selected setting on the F12's low pass filter should be either, the 3 or 6db down point of that filter so when combined with the natural rolloff point of the main speaker makes a kind of quasi crossover.

It might be worth a try setting the low pass filter at say 80 Hz and then adjusting it back to see if there is any improvement in your 40 Hz output.  

I do have them set up symmetrically I will try that first. I was thinking the swarm is the way to go. Just not sure how to implement more subs with long cable runs. Is 30' of single ended cable on a sub a bad thing? Random is better, this is what I am getting mostly.
Symmetry is death for bass. All symmetry does is ensure even more modes and suckouts. What you want is asymmetry, so the modes are all different frequencies and locations. More subs helps even more with this. More subs also means each one has to put out less total volume, because they all add together. This further smooths out response.

Long runs are no problem at all. Wire quality is much less important with subs. We just aren't that sensitive to fine differences in low bass the way we are with midrange and treble. Biggest problem guys have is getting their minds around just how different low bass is and how important it is to treat it completely differently than everything else. 

My DBA is four subs driven by 2 Dayton amps, and a 5th powered Talon Roc sub. You can easily hook them up in a chain one to the next around the room. https://systems.audiogon.com/systems/8367#&gid=1&pid=10 My one pre-out goes to the Daytons, then from one Dayton to the Talon Roc. You could go from pre amp to sub to sub, etc around the room. 

Start with one near each corner facing the wall, with each one a different distance from each corner. Its so simple when you do it you will be shocked that there's so few telling you about this. Its totally the way to go. Everyone knows it. They just won't admit it.