Total bass suck out at 40hz

Mizike, it is not uncommon to have room modes and boundary effects combine resulting in nulls of 30 dB or so.  That pretty much constitutes a total suck out, as you put it.   I assumed you have 8 ft ceilings and put your room dimensions into the amroc room calculator.  You have 4 axial and tangential room modes between 40 and 50 Hz.  Those will be broad bands and will merge into on another, resulting in a deeper null.  It's possible you have boundary cancelations due to speaker and listening position adding to this problem.  If you google Speaker Boundary Interference Response, you will find SBIR calculators that will help you figure out if speaker position is adding to the problem.  You have gotten a lot of good advice above, but I suggest you approach this systematically.   Also, you must be aware that you can't just improve the 40 Hz null without impacting other frequencies.   What you want is not the flattest 40 Hz response.  What you want is the flattest response from 20 Hz up to about 150- 300 Hz.  If you decrease your 40 Hz null by 20 db but create a null of equal magnitude at a different frequency, what have you accomplished?  So as you work on improving the 40Hz null, pay close attention to what else is going on at other frequencies.

First, optimize the positioning of your Yamaha mains with the subs turned off. Without explaining why, I would try you speakers placed with the center of the drivers 34" from the side walls.   Because your room is atypically long, an optimal distance from the front wall and an optimal seating distance from the rear wall won't be practical.  You are going to have to play around with this.

Second, optimize your seating position.   I would advise not placing your seating position in the center of the room.  16 ft or closer to the front wall, or else 23 ft or further from the front wall will probably work best for you.  Once you optimize the seating position, move the speakers again a moderate distance forward and back, and make sure they are still placed optimally.

Third, optimize sub placement.  Asymmetric placement is best.  If you set your crossover at 80Hz, you won't need to worry about loss of image or time related aberrations.   If it were me, I'd try at least one of the subs elevated off the floor, perhaps as much as 4 ft. Try one in a front corner, then try it centered between the speakers.   Try a sub along a side wall out as far from the front wall as you can get. 

I encourage everyone who gets into this to think about investing the time required to learn to use and interpret REW.  The ability to rapidly run full spectrum sweeps makes room optimization and speaker placement much easier once you get past the frustration of getting started. 

Yes mijostyn, I have come to that conclusion as well. I do think I will build a platform for one of them just to try that and see what it does. I can tell a definite volume gain while playing test tone by just leaning forward and down so I tend to agree with your thoughts on moving closer. A little more like near field listening.

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.