Hi Mandi
just because you have cysts should not stop you taking HRT.
The views on Fibrocystic breast disease is that having regular progesterone from either sequi or conti HRT can actually calm this problem down.
Estrogen on its own will make it worse but unless your able to take that (hysterectomy) then you'd be on an HRT with prog option. Even if you've had an Hysterectomy then you can opt to take prog to help your cysts.
Its up to you in the end

Trying either HRT option for 6 months to a year would show you if this was the case.
Since I went onto HRT the issues you mention have all cleared for me "sleep, hot flushes, headaches, weak bladder" and some other problems I had.

Hope that helps.