Obtaining followup clarification/feedback from referees via the editor
The simple answer is: there's no harm in sending the editor a polite email to ask. Provided your questions are broadly sensible, they're unlikely to hold a grudge against you for doing so.

However, I imagine that an editor is going to be wary of encouraging a discussion that might irritate his reviewers (who he wants to be able to use again in the future), or which appears to risk developing into a challenge to the review process itself. I suspect that you are unlikely to get a positive response unless your question is very limited in scope: for example, "Reviewer 1 comments that my results would appear to generalise the Jenkins-Smith theorem; however, I cannot find a statement of this. Would the reviewer be prepared to give me an appropriate reference?"

Have you asked a colleague to look over your reviews? Sometimes, counterintuitively, things are clearer to a reader with a shallower understanding of the intricacies of your work.