Re: On the Past Perfect Continuous and Past Perfect Simple
I agree with you on #1.
For #2, yours is grammatically correct, but I would have answered "had already worked."
For #3, yours is grammatcially correct, but I would have answered "had warned" -- although "warned" is also okay. Your is correct if the warnings were repeated.
If there is supposed to be only one correct way to write each one, it's a flawed exam.
I'm not a teacher, but I write for a living. Please don't ask me about 2nd conditionals, but I'm a safe bet for what reads well in (American) English.