I would suggest the following, if there is still time to change the design:
1. Unless you have specific things you need to store in them, create two or more shorter boxes rather than one 96" long. It's better to expose as few contents as possible when accessing external storage boxes. Shop for storage containers now (Rubbermaid, etc.) and be sure you have viable containers for the size boxes you are creating.
2. Use as much high strength aluminum T6, etc., as possible, as soon as possible. Weight is the enemy. Your planned 1/4" steel plate for the spare is much better changed to a comparable piece of aluminum or two steel tubes or channel.
3. Limit material whenever possible. You don't need to enclose the spare box, just frame it and provide a locking door.
4. Install interior lights in each box. They are very handy and you will never regret having them.
5. Garage / shop floor liner blocks work great for lining the base of the storage boxes. We used the type that locks together.
6. Standard adhesive backed rubber weatherstrip works very well for sealing the box doors. Ours has been in for 18 months and is still going strong.
7. Provide for a way to clamp down the spare. We use ratchet straps and they can be a pain. Better to have an integrated clamp that clamps down on the center hub or stud hole.
8. If you are heading overseas, design and build for two spares.
9. If you are heading overseas, you are better off with a European truck hitch on both ends and a matching tow bar than the winch. Less weight, especially when you add in the weight of the 2 Ott or larger cable for the winch motor. If you stick with the winch you must allow for all the required gear to make it viable, e.g. line extensions, tree wraps, sand anchor, etc. We use an entire long storage box just for recovery gear, almost all of which is winch related. Also, bring a spare winch controller.
10. Don't forget to allow for tie down points for the camper.
11. If your Ford flexes anywhere near as much as our Fuso, allow for some rubber blocks, 3 point pivot frame or something to isolate the camper from the frame flex.