Paradigm or JL subwoofer

Just buy the Paradigm. Sub integration is far more important then the sub itself. 
I would use the “saved” money for a highpass crossover. It will do more for you than any sub or system upgrade. The JL C-R1 is a good option and Bryston 10b-sub is another. 

I have two JL112E subs and BOTH have broken TWICE! The first time the crossovers (they have a true highpass crossover) died in both and we’re replaced under warranty. The second time BOTH volume pots failed. They were rebuilt under JL’s rebuild program and cost me $350 plus’s $130 shipping per sub…they are 6 years old or brand new now depending on how you look at it. 

Edit:

I just noticed you are using a home theater receiver/processor. You can just do this function inside your processor. If you ever go to a two channel preamp/amp you will need an external crossover to do the same thing. 
A highpass crossover will let you cut the lows out of your mains and just send them to the sub. You can then use a higher crossover on the subs because the sound will not overlap. I personally use 60hz but it will very from 40-80 depending on speaker. I find the average sized floor stander crosses over well at 60hz.
This will not only improve the bass but take a lot of the vibration out of your speakers which will clean up their sound. It will also take stress off your main amp and let it do it’s thing. Really it is a full system upgrade and I am always amazed more people don’t use them.

The E112s ($2500 each) sounds just as good as the Fathom 12s and look much nicer with the grills off imo. the driver design is a lot newer. But and it is a big but they don’t have the built in room correction. You do gain a built in highpass crossover the fathom line lacks though. 
If you have a problematic room this might matter to you. I have a large dedicated room with flexible placement so it is less of an issue for me. 

I would not buy JL audio used. They might need repaired at some point. Good sound garbage quality but they stand behind that garbage so…

Good call to stick with what you have. You will be happy with that. 
Each time my JL E112s broke they changed out all of the electronics. This last time they change everything (including the driver) but the box. I basically had 4 subs fail. My current two have been going strong for about two months…. Fingers crossed. 

Not sure about the silicone caulking. The local shop did all my repairs.