This is a classic Biztalk pattern, receiving multiple messages of different formats and updating a single back-end system (SQL database).
1. Create message for updating your SQL database.
If you use the new WCF SQL adapter you can use tables, rows, stored procedures, you can even pass a table to a stored procedure if you have SQL 2008.
2. Create a schema for each different input message type
3. Create a map from each input message type to your SQL message.
This should be easy for the comma and tab delimited files.
For the partial files you will need to implement an aggregator sequential convoy to aggregate the separate text files into a single message before mapping into the SQL message. http://abdulrafaysbiztalk.wordpress.com/2009/11/07/enterprise-integration-pattern-part-5-aggregator-sequential-convoy/
Not really sure what is happening with the SSH tunnel, but /n software have a SSH adapter http://www.nsoftware.com/products/biztalk/adapters/ssh.aspx