Charlotte somewhere in the FF FAQ is a specific ref to nightshifts and how to deal with them.

When did the CM dry up? Usually it does this just after O, or within a couple of days. since we can't rely on the temps I'd say CM is your best guide. I don't think FF pays too much attention to the early temps - I had some high ones at the beginning of my last cycle and it ignored them (also you can code them as "illness" for example0