Hi Sean,
first thank you for Enterprise subscription.
About your questions:
1) The Error 404 page ID is not the article ID, but the ID of the item you have created in ReDJ Manager under Pages 404. Here you can find two existing items. I suggest to create a new one, and put this ID into plugin. If you need to show an article, inside this item you can use a macro to get the article content. That's all!
2) After the last ReDJ version, it works well with JoomFish (both COmmunity and Enterprise). The problem is related to plugin order. Usually, ReDJ should be the first system plugin, but with JoomFish this is not enough, so there's a plugin option "Early Redirect" that solve this problem with JoomFish, so you can leave ReDJ plugin as the third one (both JoomFish plugins can be left before, as 1st and 2nd).
3) If you get problems, I can solve for you. Just send me a private message at info(at)sistemistica.it, with a temporary backend access.
Best regards,
Luigi