I this a valid combination of modules?

A Level Maths: C1-4, D1, M1
AS Further Maths: M2, S1 and FP1

Also, is it worth retaking an 85 in S1 to account for a potentially lower result in M2?

C1-4 have to go in Maths, FP1 has to go in Further Maths, the applied units will be allocated automatically to the 2 qualifications to maximise your Maths grade (and then your FM grade) - you cannot choose what goes where. The rules are that you could have any 2 of D1, M1 and S1 in Maths, or M1 and M2 (but not S1 and M2 or D1 and M2).

I thought there was a chance to allocate whichever modules (within the specs) was it AQA or Edexcel.

No, it's all bound by that gripping read I mentioned in another thread (http://www.jcq.org.uk/exams-office/entries/gce-maths-information/gce-maths-rules---guidance-for-centres). However, the rules are almost certain to give you the best option for you anyway.