M-x customize-face RET org-link RET
I understand that I can access and change the appearance of links when there's no mouse over them, but I can't find a way to change the background color and font color when I put my mouse over them. The current color combination has a really low contrast.
Use M-x describe-face RET TAB and look for a face which looks like the one you want to change. Alternatively, place the cursor on a link, press C-u M-x what-cursor-position RET (or C-u C-x = by default) and look for the name of the face for the mouse-face text property. You'll find that this face is called highlight.
Then you can change this face in the usual ways, for example using M-x customize-face RET highlight RET.
