There is a good reason for having trouble constructing present perfect sentences about events in the past. The present perfect simply is not about events in the past. It's about states in the present. A state in the present can imply an event or an action in the past, of course, but so do many other things.
If I understand your context correctly, you know someone who used to live in Siberia but now lives somewhere else. His living in Siberia is a past-tense state. His having been to the North during that time is also and necessarily a past-tense state. The tense appropriate to this context is the past perfect:
Had you ever been to the North while living in Siberia?
If you want to know about his present-tense state, then the present perfect construction makes sense:
Have you ever been to the North since living in Siberia?
The phrasing "since living in Siberia" might be interpreted as starting when he arrived there, or as starting when he left. In either case, it represents a period of time that extends to the current moment. It is a present-tense state. It works with the present tense construction of the main clause.
Have you ever been to the North while living in Siberia?
This version of the question implies that he still lives in Siberia, or perhaps that living in Siberia is an established habit and you expect him to live there again. The phrasing "while living in Siberia" has no tense of its own, but it exists within the tense of its main clause.
If you really want to ask about past events or actions, you don't want the perfect aspect at all. A past indefinite construction is appropriate:
Did you go to the North while living in Siberia?
The past tense event of going to the North is made explicit with the past indefinite construction, and implied by either the past perfect or the present perfect. Given your context, you shouldn't use "have been to".