Got the kicker 6.5" installed. Big thanks to those who helped me make a decision on this, I'm very happy with it. I'm glad I did not go through the trouble of trying to mount a larger sub in the factory location, because this kicker with my old amp is plenty loud for the jeep. Here's a few pictures I took during/after the install.
Got the center console and speaker enclosure out, and decided to polyfill while I was in there. I ended up tucking the factory wires into the enclosure before installing the new sub.
Comparison between OE speaker and Kicker.
After trimming the plastic fins in the enclosure, I mounted the speaker in there. Just a quick note, there is a portion of the enclosure for the factory amp that sticks out just a bit into the magnet. The speaker was able to mount flush with no gaps anywhere, but it's not in the exact center of the opening.
I drilled a small hole to fit the speaker wires through, then sealed the hole with clear silicone. I picked this spot based on where the amp was going to be to keep all the wires hidden.
Amp located in floorboard behind passenger seat. If you fold the backseat up it's hidden from view. When I take the backseat out I can just put a jacket over it when I park.
Here's the speaker after the install.
Thanks again for everyone's help! This set up just makes it all the more apparent how crappy the factory set up was.