You can turn off implied target buffs with a checkbox -- go to Options >> User Interface >> Targeting Windows.
Icons on page 2 of the Nav bar are not editable from within the UI (although it's an interesting idea). It would have to be done manually. But you can configure 10 additional icons on the floating Nav bar, which is a duplicate of the main Nav bar.
Chat is the only window I'm aware of that can fade out after inactivity. If your chat window has stopped doing that, click "Default opacities" in Window Settings. There is a "fade speed" setting in Options >> User Interface >> Game Windows that affects all windows. Is that what you are looking for?
Group window lookup:
