Okay. I think I've found the conformation I was looking for, although if anyone has more proof please feel free to post.
I found pictures of a very original and untouched 68 J code 4 speed for sale that was in the family since the beginning and had good pictures of the underside.
Amazingly rust free also so must have come from a dry climate and been garaged and well cared for.
I can see the flat bottom of the bellhousing which is only on the C5AA 164 bell, and without the unused boss that the 157 tooth bellhousing has.
The 157 tooth bell is not flat on the bottom and has the unused boss so it's clearly the 164 tooth bell in the pictures. (see pics below)
As a side note, I saw many pictures of 68 GT350 4 speed cars and they all had the 157 tooth bell. None of those were super original so I don't trust that yet
but if they did come that way then it's a little weird that the Shelby would have the 157 tooth C5DA-A bell and the Mustang J code 4 speed would use the 164 C5AA-B bell.
One more side note. The Kevin Marti book "Mustang...by the Numbers" only shows three 1968 Mustangs produced with the 302-2V F code engine.
Two with 3 speed manual trans and one with 4 speed manual trans. I would never have guessed that. Pretty rare if you think about it, Three cars!
I know many 68 289's actually had 302 blocks so I guess they had to use up the 289 cranks and rods before going to 302 stuff
and also saving the 302 cranks and rods for the J codes so it makes sense but still interesting.