Save as… (simple save as…) normally clears up quite a bit in the document.
However, it depends a lot on the document itself; what kind of document it is. However, JavaScript modifications rarely should cause such a dramatic growth of the file. In fact, the initial size of the document is already quite big.
Do you also "play around" with fonts in fields? If so, be aware that once a font has been specified for a field, it gets fully embedded, and it will also not be cleared out when it is not used. In this case, the only thing you can do is to take a virgin version of the document and copy the fields from the "big" document to it. You will also have to get the document-level scripts, the page actions and the document actions over to the virgin version.
It may be a good idea to use the PDFOptimizer functionality to find out what part of the document uses how much space.
Another important thing with forms is to deactivate the "save as… optimizes for fast web view" option.
Hope this can help.
Max Wyss.