Works fine for me. It's not the update. It's more likely something in your Safari preferences.
The only add-ons I've added to Safari are SafariBlock, Safari AdBlock and Safari Stand, none of which affect pdf viewing. Yes, I can scroll up and down, even with text highlighted.
I just told you how to do it.
Works for me. Even worked on PC's before the first Mouse was built to scroll with.
I understand what you are trying to do, I just tried it on 3 different computers each with Safari, Firefox and Preview, none will scroll past the bottom of the window with the mouse held down. If you click where you want to start ( do not try to highlight, let go of the button ) then scroll to where you want the end to be, then Shift Click on the end and everything between the first click and the Shift Click will Highlight and you can select or do what ever you want with the selected text.