My sister and her husband separated last year for about two months before recommitting and they are still happily married. Separation can be good for a couple who is considering divorce, and depending on the couple's situation and goals, intimacy (or cutting off intimacy) can be appropriate in relation to those goals and circumstances.

However, seems like once papers are filed, a final decision has probably been made. The 90 day waiting period seems to be in place to give the couple "one last shot" at calling it off before it is final. IMO, if you've made a "final" decision and you're so far down that road that you've filed for a state certification of that decision, the best advice would probably be to act like you're already divorced so that both parties can have practice living like they're divorced. Circumstances might be different for different people, but I think that would be a good general rule.