When looking at all available tool palettes, it's possible to switch where tools are located on the palette list by activating the Customize button. Is there an easy way to undo all such customizations, or are you limited to manually reversing each change by consulting a list of the initial tool locations?
Unfortunately, there's no way to reset the position of the tool palette, unless you completely erase your savefile and re-obtain the tools through the 9-day releases (or by changing the console's date) or by reversing each change manually as you suggested.
Anyway, to facilitate the manual labor, here's a reference for all the tools on their default position by the time everything's unlocked.
You will have to do it yourself, sorry 'bout that.