...and the question is...
Different versions of the OS have different versions of keychain.plists. There are probably also keychain.plists in HD/System/Library/Keychains. I'm not sure what you mean by "my /Library/Keychains". Is that your home Library or the HD/Library or the HD/Systems/Library?
I'm also confused by the several posts concerning Updaters for OS 11.x. Apparently, you have rooted out many files and encountered mostly more problems in the process. I have no idea of the state of your system, but if you can still boot up, I would think the use of a Combo Updater might solve more problems than continually looking around and affecting things that should only be touched by reliable maintenance tools or the OS. My Golden Computer Maintenance Rule: Just because we can do things, doesn't mean we should.
Of course, that's just my paranoid opinion.
I will say it has been interesting reading. Sorry I can't be of help.