In you first sentence, you would say “I think John has missed the 7 o’clock train. That’s why he isn’t here now”
The explanation being that there is a connection between the past and the present. John missed his train and this causes a situation in the present: he isn’t here.
In your second question, all verbs are in the present perfect except for the last one; so:
A university professor and his wife were leaving the church. It was raining heavily. The professor said, "Ha, who is absent-minded now? You’ve forgotten your umbrella and have left it in the church, but I’ve remembered mine and I’ve picked up yours, too. We won’t get wet now."
This is because the verbs describe actions that happened in the past and have a present result. In natural speech we probably wouldn’t use “have” each time. After using it for the first verb conjugation, we would probably just use past participles for the other verbs.
His wife answered, "Fine - but the trouble is, neither you nor I brought an umbrella to the church today."
The last verb “brought an umbrella” is in the simple past because it describes an action which is short and complete. It occurred in the past; it’s placed in the past by the fact that the action happened before they arrived at the church.
The tenses won’t change if we use 'left' instead of 'were leaving' because you are using inverted commas and real speech.
I hope this will help. The past tenses can be very tricky in English.