Can you show us a picture of the 'corner' of the bed (looking from the side) where the capping over the top of the bulkhead and the side of the tub meet? I'd like to see how they fit together and in relation to the rear door opening.
Did you get a pukka Doule cab roof / rear piece to do your mods?
These seem to be pretty hard to get hold of even in the UK - I'm thinking that I could wield the Tig torch and knock something up from a truck-cab roof that'd work. I recall looking at a picture in an old LRO of the 'first ever' double cab that special vehicles put together long before the official double-cab release - i'll see if i can dig it out again to see if it gives any clues to how they did it.