Unless you're forced into using certain tool (work, etc), start by standardizing on a single tool. That's one reason a lot of people like Obsidian, but there are plenty of similar tools, or you can just write markdown in your editor of choice. Then set of some sort of sync so you have it everywhere you are (mobile can be a bit tricky for some set-ups) and commit to using that method as much as possible for your notes.

You may want to do as described and link to Slack messages (etc), but just remember any external link should be treated as ephemeral. You may not have access to the Slack anymore, for example. That may mean you don't need that note either, or it may mean you lost access to a node on your knowledge graph, you have to determine whether that matters.

By starting now, at least everything going forward is captured in a way you can both own and utilize it. Then it may be a bit of a pain and some manual work to get existing notes into your tool of choice, but you can determine what needs to be in there from other tools as you go forward.