Do Mathematics modules have to be consecutive when swapping around?

I've done / doing C1, C2, C3, C4, M1, M2, M3, S1, S2, D1, D2, FP1, FP2.

Can I use M1 and M3 as my 2 applied modules for core mathematics or do they have to be consecutive? e.g. M1 and M2

You (and your school) have no choice -- the modules are arranged automatically by the exam board to make sure that you get the best possible grades.

But even so, no. Your Maths A-level will consist of C1-4 and two out of M1, M2, S1, S2, D1, D2 (where if e.g. S2 is to occur then S1 must also occur), and the rest of the modules will go in your Further Maths A-level.