At this point, the solution probably isn't something that can be solved with software (although there's a million ways you could improve user discovery across instances).

When it comes to building communities, a much more grassroots type of campaign must take place to bring people together. This can include setting up dedicated spaces, convincing network influencers to talk about it and use it, and promoting unifying causes through these newly created channels. Heck, to some extent this is something that must also be built offline, as a means to connect people in meatspace first and foremost.