I'm just starting out, and having trouble navigating space in 3 dimensions. Even when I know what coordinates I want, I have a difficult time getting there. Is there any way to target a specific X,Y,Z coordinate so I can aim for it manually or autopilot to it?
Yes, in sector map. Change axis and navigate the blinking cursor with the numpad arrows, then click on the cursor.
There are mods/scripts that make it even easier to navigate, I don't have the links to them though.