1) If you click on an input, it will highlight the module feeding it. Also, if you connect from one input to another while holding SHIFT, it will connect the moving input to the source of the other.
2) Automatically repositioning would be annoying, especially as reposition methods are usually imperfect. I assume you use Edit/Reposition as appropriate.
4) You can add a colored grid (Preferences/User Setup) which might help (or hurt). Set the grid size to 5 and select a nice restful pink for a different look.