There are some nuances I'd have to nail down. For instance... if someone orders two weekly shipments, would it be ok that they would be calculated as separate packages and wouldn't have the same combined shipping cost? It would almost be necessary since they might cancel one or the other and you couldn't guarantee the long term shipping cost savings of packaging them together.
Maybe it would be best to always calculate shipping as individual packages whenever one or more recurring items are in the cart? That way you wouldn't have to explain the discrepancy to your users?
If we nail down the precise way to solve the problem, then I think I could do it in an hour, but we would have to have the solution clearly defined and understand the limitations of any technique.