- What have you been doing since I left?
- What did you do after I left?
- What have you done since I left?
are all correct and natural, in my opinion. "had left" would seem awkward and unnatural to me in any of the three examples above. In fact i can't think of a natural sentence using "since I had left" to indicate a point in time.
Since i had left, i didn't hear the speech.
is valid, but in that case "since" means "because" and does not specify a point in time.
According to the Cambridge Dictionary's article on "since"
When since introduces an action or event at a point of time in the past, we can use the past simple or present perfect after since and the present perfect in the main clause.
When since introduces a state in the past that is still continuing in the present, we use a present perfect form of the verb after since and a present perfect form of the verb in the main clause:
"Since I’ve been back at work, I’ve been feeling great."
(The Cambridge article includes additional examples, which I did not copy here.)