I have edited the link on your Moodle page so that it opens properly on an ipad. If you have any other problems, post a message to this forum and someone in the e-learning dept. will fix it.
If you see this problem again, one way of dealing with it is to hold your finger down on the link until a menu pops up.On the menu you can choose to open the file in a new page.
I'm not sure of the answer to your second question about saving pdfs just now. I'll think about the best solution and post the answer later.
Head of e-Learning