I made a custom sealed enclosure for an 8 inch sub and put it under my from drivers seat. It has roughly 0.5 cu ft of volume and I am thinking about using a low profile 10" in the box in the future. It required a lot of measuring and fabrication, but no one even knows it's there and it doesn't take up any cargo space. It sounds great and is made of fiberglass so it's weather resistant.
I have my amp mounted in the location you're thinking about mounting your speakers on the trans tunnel . I want to move it to an ammo can console once I get that built.
My 5.25" component speakers are currently mounted in my half doors. Obviously, that's not any good if you want to go doorless. I am working on a set of full doors so I plan on relocating them in the future. Your proposed speaker location will work, but they won't correctly project staging because only one will be directed at the driver. I am going to build pods that mount in the rocker area under the doors and angle them slightly upward. This will give the correct stereo projection and allow me to run doorless. The soundbar will give better projection, but it's still not ideal.
One thing that you will want to avoid is using overly expensive components in a Jeep. They are obviously open to theft and you don't want to be bummed out if they are stolen. Hope this information will help you make your decision.