1. John took a nap after he had read a book yesterday afternoon.

2. I got up so late that I didn't catch the bus this morning.

3. Last night, Mary said she would go shopping with me when she had time.

4. I last flew kites with my friends 5 years ago.
 
5. I wrote a letter to my pen friend several days ago.

6. I got up early and had some bread for breakfast yesterday.

Please help to check the above, thanks & regards.

Omit "had" in # 1. The rest are correct.

Got it, thanks so much.

You are very welcome.

1. The sentence is grammatically correct.

2. The sentence is grammatically correct.
3. The sentence is grammatically correct.
4. The sentence is grammatically correct.
5. The sentence is grammatically correct.
6. The sentence is grammatically correct.

All the sentences are grammatically correct. Well done!