Briony, I can completely relate.
I was loving running, but first I got a weird sinus problem that was all related to a shoulder and neck problem, and then I started to get a problem with my big toe joints and it became too painful. I'm wondering now if it was hormone related, looking back.
This summer, I had terrible hay fever, which coincided with my cycles going haywire and bad ovulation symptoms and pmt...which then moved on to lower back aches...palpitations...anxiety...and now more aches.
I've had a week of feeling much better and stupidly thinking everything was going to go back to normal - so feeling 90 with a racing heart when I woke up this morning was a bit of a blow!