I found the ref5se was a more visceral, tactile preamp with a little more flesh. I also disliked strongly the volume on ref6 which came on entirely too strong out of the gate. Zero was no sound, 10 was VERY loud. Its my understanding the ref6se update addressed this.
I’m not so sure Shindo and NS5000’s have ever been in the same system LOL. Did I miss your amplification in a prior post? In any case, I doubt anything I could add to the discussion would be of value as I have no familiarity with with your interconnects or speakers. Shindo shines when properly matched but I can’t imagine Shindo and Yamaha coexisting harmoniously.