Rhythmic F12SE setup using line in

I believe that your Marantz along with the Audyssey was performing both low and high pass functions and some e.q. functions. If you are unable to incorporate the Audyssey into your current setup you no longer have any of their benifets I.e. clear. Concise, crisp bass. The only function of the three that you have left is the low pass filter on the Rythmik.

The muddy issue comes from setting the low pass filter too high. Since the KEF’s have a -6 db point at 30 Hz. Start by plugging any bass ports the KEF’s may have and then set the Rythmiks low pas filter at 30 Hz. You can then make small adjustments in the crossover point until you achieve the sound you like best.

If your preamp is a stand alone unit, you could purchase an outboard crossover such as a miniDSP, which I believe is compatible with Audyssey and very closely recreate the the same set-up you had with the Marantz.

Low, High, or Mid for your dampening? Also, are you engaging PEQ?

High dampening. There is not a PEQ unique knob. The nonLFE switch setting is 50Hz/24. My only other option is 80Hz/24. I believe the crossover max and rolloff. 

@audiorusty 

Interesting recommendation. The KEF’s do come with plugs for the rear ports. I will give that a try, while reducing the crossover. Had a similar recommendation from @soix Thanks!

I would suggest doing one thing at a time.  Sometimes adding port plugs can change the sound characteristics of the speakers, so I’d definitely try that last after everything else is dialed in.