Hi,
Could you send me a dump of your database? Because the problems you suggest seem fairly unrelated to the problems you seem to be having. The migration systems reads rows from a dooodl-only table and inserts them as posts into the posts-table using WP-core functions.
Even when the migration stops halfway through, the database is never locked (seen as the database is only read from).
The point where it asks you to install WP suggests that the wp-config.php file has been removed. This seems unlikely as physical files are never removed outside the plugin folder.
Please send me some info as to what the situation was on your server so I can investigate whether this was the result of a plugin-bug or some other interference.