It seems that I managed to solve the above problem. The solution, described below, seems to work but I am not sure if this is the right way of setting custom menus, so any comments will be appreciated.
Step 1
Create the following directory (I didn't have it out of the box).
$UserBaseDirectory/SystemFiles/FrontEnd/TextResources
Step 2
Copy the following file
$InstallationDirectory/SystemFiles/FrontEnd/TextResources/Macintosh/MenuSetup.tr
to the directory created in the first step.
Step 3
The structure of the file MenuSetup.tr is quite obvious. Find the line
MenuItem["Open", CellOpen->Toggle, Scope->SelectionCell]
and move it to the end of the menu Cell (that is, it cannot be nested, I have no idea why). It should look like
MenuItem["Show Expression", "ToggleShowExpression", MenuKey["E", Modifiers->{"Command", "Shift"}]],
Delimiter,
MenuItem["Open", CellOpen->Toggle, Scope->SelectionCell, MenuKey["o", Modifiers->{"Control"}]]
The part MenuKey["o", Modifiers->{"Control"}] is added and changes the offending binding. Restart Mathematica.
Still, I would love to have a proper documentation on configuring Mathematica including setting up own menus, initialization files, keyboard shortcuts and so on.
