you could create an object + model that attaches to the open (running).pdf instance
with the spied element of save button/option in your .pdf,proceed from there with further elements/clicks to save it wherever you want. This should be a few clicks using Navigate stages.
Same principle if you are using sendkeys; you still need to use the root element on the model that attaches/launches the .pdf.
If you haven't done this, the sendkeys are just never going to work. As to capturing the contents, I am not aware of any downloadable VBOs that will do this, I know there are some from MS Word to capture stuff in tables, etc... into a Collection stage, but not for .pdf.
You can try the sendkeys again once you are sure you are using the root element of the correct model, or you might have a go at creating your own solution using a code stage.