This is going to sound like a sales pitch, and I apologize. But with so much at stake, I strongly recommend you work with someone who has migrated a bunch of sites to Discourse, and knows how to run the gauntlet of the issues you describe, because they have done it before.
So whether us, or someone else, I would secure professional help to get your migration done right.
Happy to document all this stuff as we go, of course. Nothing we do is or will ever be a secret. But it is hard work to get it right and fix whatever needs fixing.