Hi Sam,
Are you waking up at the same time every morning? The theory goes that they are best after 3 hrs of continuous sleep, I find mine aren't affected by when I wake up, but others are.
I also find that after AF I have a secondary phase of dips in temps before I O and they rise again.
I don't have PCOS, so I can't help you with how that affects things I am afraid.
Have you considered acupuncture or chinese medicine to assist the process, lots of women use it in conjunction and I have found it really useful in regulating the cycle and steadying my temps? It doesn't work first go, but over time I have had some great improvements.