Sorry for the delay in posting, I was busy getting everything built and installed.
Well, I almost screwed up. I started adding MDF to the fiberglass mold I made, and remembered that the soft top bars rest directly on the wheel well when the top is down. So I had to basically scrap the first idea and start over.
This is what I came up with.
By the time I trimmed the fiberglass down to clear the soft top bars, I had very little left to even fuss with. I wanted to keep the sub box as shallow as the stock subwoofer, so I used the cutout lines on my all weather mat as a guide.
I made cardboard templates of the wheel well and transferred it to MDF
(It's just tacked together here, don't worry about the wood fitment)
I soaked 1/4" plywood in water overnight to soften it, and glued and stapled the hell out of it on the wheel well curves. I added a few layers of fiberglass cloth on the entire back for strength.
Here it is pre-body filler after listening to it in the Jeep to make sure it sounded ok.
Body filler and sanding prepping for carpet:
And it sounds wonderful. 500w RMS is more than enough power!