I ran [lemmony] (https://github.com/jheidecker/lemmony) to get the /all to work correctly and to start syncing communities
You shouldn't run this script, at least not in its default config. It's more work, but a much better approach is hitting lemmyverse.net and manually subscribing to a bunch of communities you're interested in.
Unless you're very careful managing defederation and blocks, it subscribes you to thousands of communities you'll never read (including the deep/dark parts of the lemmyverse posting porn/loli, piracy, and hate-speech) that will be cached on your server, re-served to the public internet from your instance, and may have legal repercussions in your jurisdiction.
It also increases the federation load your server generates by 50x or more compared to a "normal" single-user instance that subs to 100 communities or so... which doesn't make you a very good fediverse citizen at a time when federation is being flaky and overloaded throughout the lemmyverse.
... when I go to some communities and I look at the posts created before I subscribed to the community, they either don't show up or don't have the correct number of upvotes/comments...
This is expected. To a first approximation, subscribing to a community asks the sending server to forward a copy of every post/comment/vote from now on. There's no significant historical backfill (although there are a few ways to get your instance to download a particular old post, or a handful of them).
But when you first subscribe, you'd expect to be missing old posts, and then to have posts right on the border have some comments missing depending on when they were made. New posts and comments should generally show up in an orderly fashion, except for the global issues with federated replication that cause many servers to struggle to stay exactly in sync.
... when I search for communities, next to the community name is only the number of users from my instance subscribed, not the actual number of subscribers to the community.
This is expected, subscriber counts are not federated. You need to visit the community's instance to see the global sub count.