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Disclaimer: The below is PS advice, NOT Perl advice. I'd strongly recommend going to a PS forum for such help...
OK. Your Powershell code can likely handle the authentication.
Look here in your PS code:
While I am no PS guru, I AM an automation guru :) your script is creating a PS object based on the System.Windows.Forms.WebBrowser Class. Start there, and find out how to interact with the login elements on the page. You should be able to enter text into any user/passwd fields, and click a submit button, using the mentioned class and its relatives. This should be trivial considering you have already created the object you will likely need.
That should eliminate the need to manually pause and type in credentials.
In reply to Re^5: How to handle a browser window that opens up during the execution of some external program commands