Where would I get the 5mm thick foam sheet that is used to seal the surfaces within the air boxes?
Also, any of the larger pieces for connectors and joins?

if its what i think you are talking about, just go to any foam and rubber store. i was going to do it when i was doing my car, but i just wanted to get it finished! lol

Thats what I ended up doing today for the larger stuff, however, the thin stuff that is used to coat and seal the swing doors in the air box and seal the connections between the channeling has to be glued on. I tried some spray glue (upholstery builders) but as soon as you pat/push the foam it goes through the entire thickness and gets very messy, it's designed for much thicker stuff.
The original Ford stuff was stuck on with a thin type of double sided sheeting, buying double sided tape doesn't work as it doesn't like to stick properly to the foam.

**Update**I have finished what I can for now, and have sourced some of the original foam from Ford via an old acquaintance who works in supply there. I'll do the rest when I feel like scraping another mm of skin from my forearms.