does anyone know if prednisone affects estrogen levels?

Do you mean short term pulse dosing of Prednisone ie 50mg/day x 5 days or long term continuous use?

well I have been on it for 9 months...30 mg every second day...so i guess long term use...

I begin tapering in tuesday

Predisone long-term can cause menstrual irregularity, as a result it could alter estrogen levels, generally speaking. Good luck with your taper.