To answer your question directly first: you might be able to automate your process using a script written in vbscript or jscript under the Windows Scripting Host, by creating scripts that start the relevant applications and contol them via SendKeys. See some examples here, here, and many other places (search for "vbscript sendkeys" or similar in
<insert search engine name here>). Unfortunately the comments on the Microsoft documentation for sendkeys (found here) suggest that this will not work under Vista.
What is your particular need to have the documents in SWF format? The answer to that might net you some suggestions of other ways to achieve your goal if it turns out the software you are currently looking for does not exist.
One further point that may help get relevant answers: can you describe the content of the documents in question? Are they all text, a few graphics, or very graphical? A few pages each or hundreds? What is the initial size of the documents (before conversion) and the resulting sizes that are too large?