Past Perfect Progressive vs. Simple Past

I _____ (drink) coffee all morning. By lunchtime, I _____ (feel) really strange.

I had been drinking coffee all morning. By lunchtime, I felt really strange.

I _____ (wait) for hours, so I was really happy when the bus finally _____ (arrive).

I had been waiting for hours, so I was really happy when the bus finally arrived.

I _____ (see) John yesterday, but he _____ (run) so he was too tired to talk.

I saw John yesterday, but he had been running, so he was too tired to talk.

It _____ (rain) and the street _____ (be) covered with puddles.

It had been raining and the street was covered with puddles.

The boss _____ (talk) to clients on Skype for hours, so she _____ (want) a break.

The boss had been talking to clients on Skype for hours, so she wanted a break.

They _____ (study) all day, so when we _____ (meet), they were exhausted.

They had been studying all day, so when we met, they were exhausted.

When I _____ (arrive), it was clear that she _____ (work); there were papers and books all over her desk.

When I arrived, it was clear that she had been working; there were papers and books all over her desk.

Why _____ (be) the baby's face so dirty? He _____ (eat) chocolate.

Why was the baby's face so dirty? He had been eating chocolate.