HI Brian you are not missing any thing but you are thausends miles away, hahaha
i added 2 lines to boolean diff script:copy and paste. and is working.

// config: norepeat

#include "GetObjects.js"

function DoDifference()
{
var objectpicker = moi.ui.createObjectPicker();
objectpicker.allowBReps();
objectpicker.allowCurves();

if ( !GetObjects( objectpicker ) )
return;

var baseobjects = objectpicker.objects;

moi.ui.beginUIUpdate();
moi.ui.hideUI( 'FirstSelectPrompt' );
moi.ui.showUI( 'SecondSelectPrompt' );
moi.ui.endUIUpdate();

if ( !GetObjects( objectpicker ) )
return;

moi.geometryDatabase.copyToClipboardCommand( objectpicker.objects );

var subtractobjects = objectpicker.objects;

var factory = moi.command.createFactory( 'booleandifference' );
factory.setInput( 0, baseobjects );
factory.setInput( 1, subtractobjects );

moi.geometryDatabase.pasteFromClipboard();

factory.commit();
}

DoDifference();