Estrogen doesn't grow ovarian cysts. But if you have a cyst it would suggest your ovaries are still active and you are not fully in menopause. Which could explain your fluctuating estrogen levels as well.
If you feel good, I wouldn't worry about estrogen of 1000. My Newson doctor says some women want estrogen of 2000 to be okay, especially early in menopause or peri.
The guidelines are to treat by symptoms alone up to 4 pumps/100mcg.