As the combination Ctrl+% behaves as before (it toggles between Subscript and Superscript, between Underscript and Overscript), you can use it instead of any special short cuts for Underscript: Enter your Overscript first, and use Ctrl+% to enter Underscipts. Of course, this is more challenging a habit switch than the alternative (switch to the new short cut Ctrl+4, that is.)
If you wish to change the short-cut for Below from
Ctrl+4 to Ctrl+=
once-and-for-all, you need to do some editing in two text resource files in the directory
$InstallationDirectory\SystemFiles\FrontEnd\TextResources\Windows
First, in the file MenuSetup.tr find the following line that assign the Ctrl+= short- cut to Free Form Input:
MenuItem["Inline Free-form Input",
KernelExecute[AlphaIntegration`LinguisticAssistant[InputNotebook[]]],
MenuKey["=", Modifiers->{"Control"}], MenuEvaluator -> Automatic],
I modified the last line above by adding an additional modifier key as follows:
MenuKey["=", Modifiers->{"Control","Command"}], MenuEvaluator -> Automatic],
to assign Ctrl+Alt+= as the new Wolfram|Alpha short-cut.
Next, you can change the following lines in the same file similarly:
MenuItem["&Above", "Above", MenuKey["7", Modifiers->{"Control"}]],
MenuItem["&Below", "Below", MenuKey["4", Modifiers->{"Control"}]],
The second file is KeyEventTranslations.tr in the TextResources directory. It shows the current key event short-cuts:
Item[KeyEvent["7", Modifiers -> {Control}], "Above"],
Item[KeyEvent["&", Modifiers -> {Control}], "Above"],
Item[KeyEvent["Keypad7", Modifiers -> {Control}], "Above"],
Item[KeyEvent["$", Modifiers -> {Control}], "Below"],
Item[KeyEvent["4", Modifiers -> {Control}], "Below"],
Item[KeyEvent["Keypad4", Modifiers -> {Control}], "Below"],
Item[KeyEvent["%", Modifiers -> {Control}, CellClass -> BoxFormData], "Otherscript"],
I added the following line to this portion of the file
Item[KeyEvent["=", Modifiers -> {Control}], "Below"],
Now I have both the new short cut Ctrl+4 and my old friend Ctrl+= for Underscript so that I can phase out of my old habit at my own pace:)
Of course, you need to save the files after your changes, and re-start Mma for the changes to take effect.
Caution: Casual playing with the resource files may be dangerous. It is easy to get carried away and corrupt your installation. Make backups before changing any file.