Hey Jeff - I think I found the PERFECT tool bag for your swing-down overhead molle panel design. I recently switched to this tool bag, after being impressed by these guys who can sew so well:
Video. And here's some more product specs:
Tool Bag
You can see that the the bag has a molle straps on one side and a quick access pocket on the other, for the tools you always need to grab often. Best of all, it opens like a book, which would be perfect for your swing-down panel. It could stay securely mounted while you access the tools you need.
I set up my version of this tool bag with six different categories of tools, each in its own zippered bag. Best of all, since your swing-down panel isn't available for sale (yet), I can confirm this bag does fit in that dead space between the roll cage and hard top that I am always trying to find a use for. No more wrench roll and bulky tool bags taking up space in the precious cargo zone!
Hopefully this is helpful to others looking for a similar solution, and eagerly awaiting the chance to purchase your swing down panel, like me!