Merging communities might be hard, but maybe redirecting a community to another instance? this would also allow people to move communities from one instance to another, which would allow large communities to have dedicated instances, or to consolidate related communities under the same instance.
Allowing communities to exist across multiple instances is going to be a nightmare now that I think about it, like how will moderation work? I can already see it becoming a new way to spam. Create your own lemmy instance, spam a post, and make it so that no one can delete it. It'll cause instances to disable open federation, which would mean we'll end up with only a few allowed instances
I'm only just now learning more about federation, so I'm no expert.
Is your instance setup to use NTP? federation requires fairly accurate time from my understanding, and shared hosting normally drifts quite a bit, which might be where your "Header is expired" issue comes from. It could also have something to do with your instance not processing incoming federation stuffs fast enough I think?
There is a chat space at https://matrix.to/#/#lemmy-space:matrix.org with people that run their own instances, which might help answer these questions