For 1, can you select those draggable value label things (like "goals" in the video)? If so, can you copy-paste them to achieve the same thing as a drag?
For 2, I've tried solving this problem by adjusting the scroll position to compensate for changing element sizes higher up on the page, but that never worked well enough for me to ship it. I've compensated by basically removing things from the DOM when they're outside the view, so that they can't mess with scrolling, and then reinserting them into the DOM in response to a user action. I don't think that'd work in your case, though. So perhaps the idea of pulling controls out of the main flow is the best bet. You've certainly got a lot of horizontal space to play with in your layout, so you could maybe carve off room for a panel along the left or right that could house vertical sliders and other controls. * shrug *