Rhythmic F12SE setup using line in

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. 

Out of curiosity are you experiencing any differences when making a change to the settings?

I have two Rythmiks of this make. I have done a lot of work to dial in my subs (I have a third REL). Ultimately, the best thing to do was buy a mini DSP and integrate subs that way. Highly recommended.

https://www.minidsp.com/applications/digital-crossovers/194-subwoofer-integration-with-minidsp

I would prefer to dial in my sub without the use of the minidsp. They appear to work via ADC then back to DAC to do the sound processing, something I avoided  (NAD, Anthem, Lyngdorf etc) when purchasing my preamp. Help me if I am wrong. If I was to go that route, it looks like the minDSP FLEX is the one I should choose. Thanks!

I would prefer to dial in my sub without the use of the minidsp. 

I totally sympathize and tried for a very long time -- arduous, even onerous work -- to measure, move, listen, dial in and out, etc. to get the bass right. A good friend of mine who's been an audiophile for 30 years with an incredible and well-designed system (he also builds audio) has DSP for bass. It really does not "pollute" the sound in the way that many worry about for the higher registers. Keep in mind, this is limited to the subs only.

In other words, the benefit gained by dialing in subs (and room) far outweighs the (actually small) detriments of adding dsp to the system. For me, this was evident enough to help me reconsider and reject my bias against dsp.