Some ideas:

One question per email?

Something like Trello, using each card as a question, and three columns (unanswer? re-ask? finished?)

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In case the questions need to be in a block because they are related and need some background, try to make each question easy to distinguish. Like

* First question?

* Second question?

* Third question?

(I think that in some case I number them so it's 100% clear, but I use this with coworkers that can't fire me :) .)