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Which reported speech version would be the best response?

Q: Marcia said, 'I have been waiting for you for over an hour.'

1) Mary told me that she had been waiting for me for over an hour.

2) Mary told me that she was waiting for me for over an hour.

3) Mary said she had waited for me for over an hour.

I know the first sentence is definitely the correct one here, but what's the difference between "was waiting" and "had been waiting"? They are both perfect past continuous, are they not? I remember reading in a grammar book, "I was eating when Bob came in" and it was used to describe perfect past continuous. And what is wrong with the third sentence? How does it differ from the other two sentences? Is it ebcause the first two sentences stress the duration of Mary's wait?

Apologies if I've asked this before. I don't remember if I have or haven't, but it seems like I have.
Comments  
Nos. 1 and 3 are correct. No. 2 is wrong.

Cheers
CB
Why?

If this reported speech takes place several days later - someone asks "Why was she so angry when you got there?" and that's the answer. Maybe this is part of tense simplification, since the context makes it clear the order of events.
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Because, when you want to emphasize on a particular situation or something that had happened before another situation occured, you would use had.
"was waiting" is past continuous tense.
mudclay "was waiting" is past continuous tense.
Yes, it is. Did you have a question about that?
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can you give me simple example to use was/had bennn