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Per the '69 PIM, the 5/16" x 2-5/8" lower passenger-side water pump bolt/stud that goes to the block should be a bolt for non-A/C cars and a bolt with stud head for A/C cars. I have attached the picture of the PIM.
I have also attached a picture of the bolt with stud head for reference.
Were cars actually built per the PIM or did everything leaving the factory have the bolt with stud head? I can't remember ever seeing just a bolt in that location even on some non-A/C cars, though I'm no expert.
This is just a guess on my part, but I'm thinking it all depended upon where the car was assembled. A dealer from the '60s got his A-body cars from either Lansing or Fremont (Oregon dealer). He told me the quality control at the Lansing plant was outstanding and that he much preferred Lansing cars over Fremont cars and that Fremont cars often needed "help" once they arrived at the dealership.
I have a '68 4-4-2 (Lansing) and a '69 4-4-2 (Fremont) and I believe that I see the difference as well. The Lansing car was pretty much by the book when I took it apart and then put it back together again. I see marked differences in the Fremont car - rubber plugs missing, trim piece screws missing, engine dressed for a manual transmission car when it is an automatic, poorer quality finish with the trunk spatter, a missing grommet for the speedometer cable, poorer fitting original carpet, just to name what I can remember off the top of my head.
I believe the same thing could be possible with the stud bolt you are addressing.