I've poured over the Chassis Service and Factory Assembly Manuals and can't locate anything regarding the lock cylinder assemblies. It's probably in the Fisher Body Manual, which I don't have and/or cannot seem to locate. Anyhow, is the rod supposed to be kinked like this? (1967 Cutlass Supreme)

 

No can help. Manuals don't go back to '67.

 

I think it is kinked up and down, but it is flat left to right; yours looks bent.

 

The holes look to line up and needing to be straight

 

Your rod is the exact shape as the one in my 66 cutlass. I have parted a few cars and all were bent just like the one you have.
most aftermarket lock cylinders come with a straight rod.

 

Yes! That kink needs to be there. I recently replaced the trunk lock in my '67 and tried without success to get the rod that came with the new lock to work. You know, because it was clean and purty. Once I put the original rod back in, smooth and easy. I haven't been able to find a lock retainer yet though, mine is pretty rusted and the screw tabs are missing.

 

Well..... I straightened the rod in the vise; seems to work well. Got me.
On the other hand, I had no idea what screws were used to hold the retainer in because they weren't even there. I tapped the holes for 10-24 stainless pan heads.

 

If you feel ANY resistance to turning the key, put the kink back in. It truly made a difference to mine. The screws were in my retainer when I took it apart but the tabs they went through simply disintegrated as loose rust when I took the screws out. Mine had short, self-tapping sheet metal screws. They are very rusty as well so they will be replaced if and when I ever find a whole retainer. Truth be told, I haven't really spent much time looking for one though. The retainer fits tightly and I don't close the trunk lid hard enough to disturb it.