Just wanted to post an update, I was able to fix my issue by disabling Cloudflare and now federation seems to work fine for my instance. I'll leave this post up in case anybody else runs into my problem in the future.
this post was submitted on 19 Jun 2023
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Cloudflare shouldn't impact federation at all. I have my instance behind Cloudflare and it works fine. If disabling Cloudflare made it work for you, it might be that the DNS records did not have enough time to update. Or maybe it was HTTPS related and you needed to change some Cloudflare SSL/TLS settings.
When I set up my instance, I don't remember having any trouble with the Cloudflare proxy whatsoever. It's completely compatible with Lemmy.
Maybe something with WebSockets? Try creating an instance on your local machine and see what error it gets when it tries to access your real one.
Are you using Docker?
Yup