Yes, E2 can affect joints and cause joint pain. I assume you're taking an AI?
For me personally, my joints and back hurt when my E2 is in the 20's. I used to get testosterone pellets inserted every 4 months or so. I'd always know when I needed more pellets when my joints would start hurting. What was happening was my E2 was in the 20's when my T was low, then I would get a new round of pellets inserted and my E2 would rise to 40-50'ish and all pain would go away.
Now I'm on injections and the same thing would happen to me if I took too much AI. Joint pain!! I'd say lower your AI dose.