Need to automate loading subfolders into stacks + action

You could give this a try...

#target photoshop
app.bringToFront();
var win = new Window( 'dialog', 'Auto Align and Blend' ); 
g = win.graphics;
var myBrush = g.newBrush(g.BrushType.SOLID_COLOR, [0.99, 0.99, 0.99, 1]);
g.backgroundColor = myBrush;
win.orientation='row';
win.p1= win.add("panel", undefined, undefined, {borderStyle:"black"}); 
win.g1 = win.p1.add('group');
win.g1.orientation = "row";
win.title = win.g1.add('statictext',undefined,'Auto-Align and Blend');
win.title.alignment="fill";
var g = win.title.graphics;
g.font = ScriptUI.newFont("Georgia","BOLDITALIC",22);
win.g5 =win.p1.add('group');
win.g5.orientation = "row";
win.g5.alignment='left';
win.g5.spacing=10;
win.g5.st1 = win.g5.add('statictext',undefined,'Please select output folder...');
win.g10 =win.p1.add('group');
win.g10.orientation = "row";
win.g10.alignment='left';
win.g10.et1 = win.g10.add('edittext');
win.g10.et1.preferredSize=[350,20];
win.g10.et1.enabled=false;
win.g10.bu1 = win.g10.add('button',undefined,'Browse');
win.g10.bu1.onClick = function() {
  outputFolder = Folder.selectDialog("Please select the output folder"); 
 if(outputFolder !=null){
  win.g10.et1.text =  decodeURI(outputFolder.fsName); 
  }
}
win.g15 =win.p1.add('group');
win.g15.orientation = "row";
win.g15.alignment='left';
win.g15.spacing=10;
win.g15.st1 = win.g15.add('statictext',undefined,'Please select top level folder...');
win.g20 =win.p1.add('group');
win.g20.orientation = "row";
win.g20.alignment='left';
win.g20.et1 = win.g20.add('edittext');
win.g20.et1.preferredSize=[350,20];
win.g20.et1.enabled=false;
win.g20.bu1 = win.g20.add('button',undefined,'Browse');
win.g20.bu1.onClick = function() {
  topLevelFolder = Folder.selectDialog("Please select the top level folder"); 
 if(topLevelFolder !=null){
  win.g20.et1.text =  decodeURI(topLevelFolder.fsName); 
  }
}
win.g200 =win.p1.add('group');
win.g200.orientation = "row";
win.g200.alignment='center';
win.g200.bu1 = win.g200.add('button',undefined,'Process');
win.g200.bu1.preferredSize=[220,30];
win.g200.bu2 = win.g200.add('button',undefined,'Cancel');
win.g200.bu2.preferredSize=[220,30];
win.g200.bu1.onClick=function(){
    if(win.g10.et1.text == ''){
        alert("No output folder has been selected!");
        return;
        }
    if(win.g20.et1.text == ''){
        alert("No top level folder has been selected!");
        return;
        }
    win.close(0);
var folders =[]; 
folders = FindAllFolders(topLevelFolder, folders);
folders.unshift(topLevelFolder);
for(var f in folders){
var PictureFiles = folders.getFiles(/\.(jpg|jpe|dng|bmp|tif|tiff|psd|crw|cr2|exr|pcx|nef|dcr|dc2|erf|raf|orf|tga|mos|pef|png)$/i);
  if(  PictureFiles.length < 3) continue;
  for(var p in PictureFiles){
      open(PictureFiles
);
      if(p > 0){
          try{activeDocument.mergeVisibleLayers();}catch(e){}
          activeDocument.activeLayer.duplicate(app.documents[0]);
          app.documents[1].close(SaveOptions.DONOTSAVECHANGES);
          }      
      }
        selectAllLayers();
       autoAlign();
       autoBlend();
  var saveFile = File (outputFolder +"/"+decodeURI(folders.name) + "_pano.jpg");
  SaveJPG(saveFile, 9);
  app.activeDocument.close(SaveOptions.DONOTSAVECHANGES);
    }
}
win.center();
win.show();
function selectAllLayers(layer) {
if(layer == undefined) layer = 0;
activeDocument.activeLayer = activeDocument.layers[activeDocument.layers.length-1];
if(activeDocument.activeLayer.isBackgroundLayer) activeDocument.activeLayer.isBackgroundLayer = false;
var BL = activeDocument.activeLayer.name;
activeDocument.activeLayer = activeDocument.layers[layer];
    var desc5 = new ActionDescriptor();
        var ref3 = new ActionReference();
        ref3.putName( charIDToTypeID('Lyr '), BL);
    desc5.putReference( charIDToTypeID('null'), ref3 );
    desc5.putEnumerated( stringIDToTypeID('selectionModifier'), stringIDToTypeID('selectionModifierType'), stringIDToTypeID('addToSelectionContinuous') );
    desc5.putBoolean( charIDToTypeID('MkVs'), false );
    executeAction( charIDToTypeID('slct'), desc5, DialogModes.NO );
};
function autoAlign() {
    var desc16 = new ActionDescriptor();
        var ref8 = new ActionReference();
        ref8.putEnumerated( charIDToTypeID('Lyr '), charIDToTypeID('Ordn'), charIDToTypeID('Trgt') );
    desc16.putReference( charIDToTypeID('null'), ref8 );
    desc16.putEnumerated( charIDToTypeID('Usng'), charIDToTypeID('ADSt'), stringIDToTypeID('ADSContent') );
    desc16.putEnumerated( charIDToTypeID('Aply'), stringIDToTypeID('projection'), charIDToTypeID('Auto') );
    desc16.putBoolean( stringIDToTypeID('vignette'), false );
    desc16.putBoolean( stringIDToTypeID('radialDistort'), false );
    executeAction( charIDToTypeID('Algn'), desc16, DialogModes.NO );
};
function autoBlend() {
    var desc17 = new ActionDescriptor();
    desc17.putEnumerated( charIDToTypeID('Aply'), stringIDToTypeID('autoBlendType'), stringIDToTypeID('maxDOF') );
    desc17.putBoolean( charIDToTypeID('ClrC'), true );
    executeAction( stringIDToTypeID('mergeAlignedLayers'), desc17, DialogModes.NO );
};
 function FindAllFolders( srcFolderStr, destArray) {
 var fileFolderArray = Folder( srcFolderStr ).getFiles();
 for ( var i = 0; i < fileFolderArray.length; i++ ) {
  var fileFoldObj = fileFolderArray;
  if ( fileFoldObj instanceof File ) {   
  } else {
         destArray.push( Folder(fileFoldObj) );
  FindAllFolders( fileFoldObj.toString(), destArray );
  }
 }
 return destArray;
}  
function SaveJPG(saveFile, jpegQuality){
jpgSaveOptions = new JPEGSaveOptions();
jpgSaveOptions.embedColorProfile = true;
jpgSaveOptions.formatOptions = FormatOptions.STANDARDBASELINE;
jpgSaveOptions.matte = MatteType.NONE;
jpgSaveOptions.quality = jpegQuality;
activeDocument.saveAs(saveFile, jpgSaveOptions, true,Extension.LOWERCASE);
}