I’ll take a stab at this 
1) what are you best practices for creating subscriber engagement?
At least once a month, I post something that directly asks for feedback from my Patrons and explain what I am doing/why I’m asking. My Patreon is for my blog, which is a very niche topic (handmade soap - how to/recipes/tutorials, and then small biz management for soap companies - marketing, email newsletters, blogging, websites, entrepreneurship, etc.), so these ideas may not work for you, but some of my previous posts were asking for input on upcoming content (like what you do/don’t want to see, what topics should I cover, do you have input on this specific topic so I can quote & link you, what are you struggling with, I’m hosting a giveaway which of these things do you want to see, I’m changing up my Patreon reward levels what do you think, here’s a new article I’m working on - didn’t I forget anything, etc.)
Every month, I send at least one blanket message to all my Patrons. Whether that’s one message to all processed pledges that says “Hey, thanks!” or it’s a blanket message to a group of Patrons to make sure they see a specific post, etc. I think this helps foster the give and take relationship of a content creator and it’s community.
I also link content I’ve created elsewhere so Patrons have “one place” they can catch up, which helps turn my Patreon into their main feed - so they don’t swing by when they remember.
2) what is the best way to organize bonus content so that it’s easily discoverable by new subscribers, and does not get lost with all the free content being posted?
I utilize the crap out of Patreon’s tagging system, I also have a video that shows folks how to use it. In both my Patreon description and my Thank You page, I link to reward-related tags. Before the tagging system, I also kept a Master List where I linked all content based on rewards level and linked that in both my description and thank you page.
You can see my Master List here: https://www.patreon.com/posts/5102910
3) Is a message board like the one we’re using here critical for fully engaged community? If so, are you using a third party provider for that, and does that have a negative impact on your Patreon subscriptions?
I don’t think so! I do use third party services to facilitate communication with Patrons - both sending direct emails at times (by snagging emails from the Patron Manager), but I also host monthly webinar workshops with my Patrons through another service and that’s helped foster more community.
I think the biggest thing is just inclusion - do what you can to get them involved, nothing is too stupid to share with them - I find most of my Patrons support me because it gives them more personal access to me as a Creator instead of generically buying something from my website, etc. (for instance, when I was sick last year, I let them know - no one else got that kind of “FYI”). Communicate and involve them as much as you can in your Patreon campaign’s purpose - whether that’s taking their ideas or feedback, or just checking up with them as people.