I don't have either one of those problems. You have something else going on there.
It's a unibody 2008 MacBook Pro and with two-finger scrolling I cannot scroll over a youtube video, I can if the cursor is next to the video. This happens in Safari only. I can scroll over it when I use the Magic Mouse instead of the trackpad.
Maybe it is one of the extensions, I noticed that "AutoPagerize" (Productivity) causes beach balls when I reload MR and try to scroll before it's done loading the page.