Anyone now where the game stores the mod list and its load order?
I reinstalled the game, but have now idea what order I had the load order. So now the game crashes all the time when leaving Windhelm. I took backup of the files in MY Document and %appdata% and hope its in there somewhere, but have no idea.

The file for the load order is what the game uses to determine load order. That file isn't going to help you. Basically, if you were managing things manually and don't have your backups you need to redo the work.