Kicad Version 5.1.0 Missing shortcuts
This is a few questions, so I'll list the answers in the numerical order you have asked the question.


After reading the netlist, your footprints should be spread automatically.  Therefore this menu item was removed.  Note that the preferred method for updating pcbnew from eeschema is now "Tool->Update PCB From Schematic (F8)".  This avoids the netlist step.
There is no program-based way to edit groups of pads from the board editor.  You can edit the footprint and then replace all of the footprints on the board with your edited version.
When you open a footprint from the board and change it, those will be saved to the footprint on the board




There is no general way to change the toolbar.  Add your vote to this bug report if this feature would be important to you (just check the "This affects me too" button at the top).