It’s possible the rumble and flutter are being amplified from feedback. Especially with a sub, it can push out a lot of energy to excite resonances on your rack, plinth, tonearm, etc. If that’s the case, better isolation will help a ton. You can "easily" test if this is the problem - by listening through headphones (speakers off, subs off) and seeing if you enjoy much better signal-to-noise ratio.
I’ve heard inadequate isolation manifest as a rumble sound, and as a hum that sounds much like a ground loop. These types of feedback are particularly insidious because they can get to a point where they runaway (keep increasing), which is dangerous.
Also dangerous is woofer flapping (subsonic energy), ESPECIALLY on those KEF’s! Unlike per cones, those drivers cannot tolerate excursion at all past their limits (search for ample photo evidence of busted KEF drivers). Thankfully you’re protecting them with a sub (assuming you run a high-pass filter on the KEF’s - if not you need one or you run risk of breaking the drivers), but too much energy isn’t good for the sub either and it will contribute greatly to feedback into the table.