CR File Transmission

I am looking for solution to perform various forms of automated file transmission from/to our website, including but not limited to email, secure email (browser based), ftp, secure ftp and browser based upload/download. Website upload and browser based email transmissions could conceivably require automating keyboard strokes. Files need to be associated to particular users of our website. I will need the ability to poll for or recieve response files by any of the above methods automatically and associate these files to the current user. File naming conventions for user identification may not be applicable for every type file; more likely individual client folders/mailboxes would be a possible solution. Response files will be asynchronous and may arrive or be ready for 'grabbing' at any time up to a week or more after transmission.