User#2 is the main admin for the board - it should never be deleted. Not sure how yours is missing. Did you import from Classic? You can register a generic "admin" type user - make it an administrator and change it's user number to 2. Then all the missing PMs will appear.
Likewise with the missing forum, is the user number who holds the last post in that forum missing in the user's table? You didn't say what version, but this was a bug back in ~6.3 I believe. You have to make a new post to the forum to get it to appear (use the URL newpost.php?Board=keyword)
