I’d suggest you make a ticket on Trac with a diff for this. Your account from here acts as your login and it is more likely that this change will be considered if it is there.
This is a bug which will be fixed in the next release (http://trac.wordpress.org/ticket/7316). The links themselves haven’t actually been deleted (should still be on the manage links screen).
Moving them might allow you to rename the blogroll category otherwise there is some other issue with your tables.
Interesting, not sure why that line would cause the error. Your fix actually introduces a syntax error as it introduces an ( which isn’t closed.
That file is concerned with updating plugins automatically. If you don’t have any plugins or always manually update them, you should be fine.
