Unfortunately, then, this will probably require some custom development.
Changing that old code to @
dvsDave won't actually do anything because it's not until a post is saved that the @
dvsDave is converted to [USER=1107]dvsDave[/USER].
The custom development would, I envisage, a rebuilder that looks at the content of every post on your forum, finds a [USER]username[/USER] BB Code in the message content, performs a regular expression to get the username, performs a database query to fetch the User ID from the username (usernames are always unique) and if a matching user ID is found then it could convert it to the new style BB code in the format of [USER=user_id]username[/USER].
Failing that, you might just want to use the Post Content Replacement tool (it does work on 1.2) to remove the [user][/user] bits, just leaving the username.
You could, I guess, convert it to @Username but, again, it isn't converted to a clickable link until the post is saved.