Now when I try to start FS9, I get an error message saying this application cannot run when debuggers are active...
This because you are probably using an old version of the Addon Manager installer, or an old version of a scenery you had, that wasn't compatible with the >2GB patch and didn't checked which FS9.EXE you had. This has been fixed in later version.
I can click on OK, then I am told that my Zurich and O'hare are old and out of date and will not run, even though they are both the newest versions.
This just confirm what I'm saying: either the scenery is outdated, or the Addon Manager is. You end up in this situation, if you install a new version, and try to go back to the old one, without first uninstalling everything.
Also, the current version will always automatically get the very latest versions, which are guaranteed to work, but you need to have everything updated. If you mix-match releases, it will not work.
So, uninstall everything, then reinstall only the most current versions.
I have completely uninstalled JFk, including the addon manager, then re-installed the stand alone addon manager in an attempt to at least get Zurich and O'hare working again, but no luck, they are gone.
Of course they are: if you keep trying to use old Zurich / O'Hare with the new Addon Mananger, they will never work: the program will give you a warning, like you said. So, the solution is not to downgrade the Addon Manager trying to use the old versions, the solution is to update the scenery,exactly like the program advised you to do. If you download again current Zurich and O'Hare installer, they are guaranteed to work with JFK.