I see that you understand what's going on and your explanation makes sense. Since the previous admin account is gone (probably not really gone; just no longer known by its name), the current state of the system is a result we might have expected.
I now think that permissions are not the problem. Instead, directory and file ownerships are the problem. This can be changed with the chown command. This command would change the ownership and group ownership of one application and all of its files:
Code:
sudo chown -R root:admin /Applications/Calculator.app
This would change it for all applications:
Code:
sudo chown -R root:admin /Applications/*.app
Changing them to root:admin should produce ownership by "system" as shown in the Get Info window. Another choice for some or all applications would be to change them to
wifeusername:admin where
wifeusername is your wife's user name, since that's the sole user who is an administrator.
These are my questions.
One: Assuming that I don't make any errors with the with the terminal command could/would sudo chmod -R 777 /Applications do any harm if I did a repair permissions afterwards and would it change everything inside the app folder.
It is possible (but I don't know if it is likely) that an application would be unhappy to have particular files with permissions 777. I know certain server-style applications that are unhappy to find some of their files having world-writable permissions, but I can't think why a typical Mac OS X application would mind. Repairing permissions can correct permissions only for applications whose correct permissions are in a manifest, which should be true for all of the Apple ones but possibly not for some third-party apps you installed. So the answer to your question is maybe.
Two: Could terminal also be used to change the Application folder and everything in it to Owner: System, Group: Admin and if there is only a single admin user for the computer does it matter if the owner of a self installed app is System, or does it have to be the user?
On a one-user computer it shouldn't matter which you choose. I haven't tested this, but I would assume that if you set them to root:admin, you will be prompted if you try to replace an application. If you set them to
wifeusername:admin then when logged in as
wifeusername I'd think you could replace them successfully without getting prompted. I think getting prompted is to be preferred, meaning that root:admin is best.
Three: My ideal Terminal command would be to change everything inside the app folder to Owner: me, User: Group and all the permissions to be 777 then I'd do a repair permissions afterwards
I suggest trying the chown command on one application that gives you trouble, as a test. Perhaps that alone will be enough to solve the problem.
A hindsight lesson from all of this: As a general rule, it's best not to remove the account of the original administrator, or a user who has installed applications you will keep using. If you don't want an old account to be used, change its password but leave the account defined.