Sounds good. Very interesting on the squashed nut - makes sense.
I've got the similar-but-different 3.0i, and have the manifolds off right now. On that engine, they are 11mm hex nuts on M7-1.0 threads, copper plated steel (I assume - they look copper, but are magnetic).
When I pulled them, of the 16 studs (different layout from the 3.0d), I think 11 studs came out of the head rather than the nut coming off the stud. And I think I did this all from above.
Regarding getting the 12mm deep sockets, I swear I used about half a dozen different options getting my nuts/studs out, and I needed all of them. Ratcheting 11mm wrench, 7/16" wrench, solid closed end angled 11mm wrench (that was thinner that the other options), short sockets, long sockets. I wish I had a swivel socket in an 11mm (I do in 10 and 12), but that is such a rare size.
Since it is such a tight fit on my engine, I sometimes had problems fitting 3/8" drive sockets, where a 1/4" drive might fit. And every one of those 16 nuts was a different adventure. Some took less than a minute, some took 30 minutes. Wow.
Also, I don't have any E12 around there, but it sounds like you do. In case there is a place where you can't fit a regular E12 socket, I recently figured out that a Craftsman 3/8" Universal ratcheting wrench is a PERFECT fit on the pretty-common E12 head. This is a wrench designed for a 3/8" hex head, but they make it "universal" by making it with 12 bumps, allowing it to fit hex, square, torx, etc. You'd generally want just the regular E12 socket, but when that does not fit ...
Here it is:
https://www.sears.com/craftsman-3-8-...p-00920601000P
Attachment 74068
Of course much cheaper when buying a set. The 10mm version works pretty well too, but is slightly looser than the 3/8".
Those gaskets look interesting. What are those extra holes on the side for? Alignment of some sort?