I know our minds tend to think the worst but most ovarian cysts go away on their own. And most are benign (non-cancerous), even ones that look suspicious and have to be surgically removed. Do you mean the ovary is 89mm not 89ml? 89mm = 8.9cm which would seem reasonable being that the cyst is 6.4cm. The 2cm growth in your endometrium may be a fibroid since those are very common and rarely cause for concern since they're benign. Many women have an antiverted uterus.
Hashimoto's can mess with the menstrual cycle. Optimizing your thyroid meds may help the bleeding. I don't know if thyroid issues play into ovarian cysts or not.
I had a 9.5cm ovarian cyst that was benign but I was overtreated. My gyn removed my uterus and both ovaries and I've been suffering the nasty effects ever since (11 years).
Best of luck to you in getting proper treatment. Keep us posted.