My Sonus Faber Amatis have weak bass even though I'm running ML 536s--800 w/ch into 4 ohms

Walk around in the room and determine if some satisfactory bass output is present at a location other than your listening location. Move speakers a bit closer to the front wall and walk around some more.

If you are sitting on top of modal nulls, you might start to wonder where all the bass went. If you can’t move your listening position, correct positioning of subs and sub phase adjustment would be the way to address such nulls.

Do a battery tap on each speaker and see if the woofers are moving in the same direction. (check if some Italian guy wired something wrong when he was coming out of riposo)

etc

Did you try a different amp? Some half broken amps can make all the bass disappear, depending on the issue. Take it to some local tech (if you are not set up to bench stuff at home) and check it out. Here’s an example

https://www.youtube.com/watch?v=M8vhVTQ1cLo

On a positive note, those KEFs are nice subs.

It could also be that your Amati is a slightly bass flaccid speaker overall, with emphasis on looks and mids "sweetness", tailored for Diana Krall, not MC Ren.

Did I miss the part where you told us about speaker placement? How far off the wall behind them? How far apart are they? How far away do you sit from them? Are you using the Naim as a streamer and the Classe as preamp and Dac? I’m not a big fan of Naim and I’m not so sure the Classe is the right preamp for the Levinson's,, If it was me I’d look for a Levinson preamp. At then you’d know that impedance and phase are correct, Then a appropriate Streamer and Dac, I just think there’s some mismatches in your equipment and maybe speaker placement 

i have a room that is remarkably similar in terms of dimensions and the back being half wall and half open to the kitchen. In my case i have high ceilings with irrigular angles above which is overall beneficial.  Keep in mind, large rooms are always much harder to fill with Bass AND that open back wall means that there are no back wall for the bass to bounce off and get enforced.  Walk around the room.  Pay attention to see if the bass is stronger as you are near the side walls or in that one back corner.  Does it lessen as you get to that area that is open in the back.  i agree with  pkatsuleas it is likley more about the room .  i chimed in because my room is so similar.

Here’s an example

https://www.youtube.com/watch?v=M8vhVTQ1cLo

As an aside, Duality Repair, the YouTube channel linked above, is one of the best if not the best electronics repair channels on YouTube. 

Too bad he doesn't post more regularly. He sometimes goes months without a new episode.

+ "Found Nordost to be light in the bass."