Running Para Numbers

The following script will set up an object style and paragraph style for the margin numbers (mimicking the format from your template) and will insert the numbers automatically (as an anchored object). If you want to update the appearance/position of the margin numbers, edit the paragraph style and/or object style.

The margin numbers will not automatically update when your pages shift; however, you can run the same script again and it will delete the existing margin numbers and insert new ones. Let me know if you run into any issues.

app.doScript(Main, undefined, undefined, UndoModes.ENTIRE_SCRIPT,"Run Script");
function Main(){
// Declare variables
var myDoc = app.activeDocument;
var myPages = myDoc.pages;
var myPage;
var myFrames;
var myFrame;
var myParas;
var myPara;
var headerStyle = myDoc.paragraphStyles.item("Note_para");
var marginNumberParaStyle;
var marginNumberObjStyle;
var noteNumber;
var ip;

// If "Margin_number" para style doesn't exist, create it
if(myDoc.paragraphStyles.item("Margin_number") == null) {
    var paraProps = {
        name: "Margin_number",
        appliedFont: "Minion Pro",
        basedOn: myDoc.paragraphStyles.item("[No Paragraph Style]"),
        fillColor: myDoc.swatches.itemByName("Paper"),
        fontStyle: "Regular",
        justification: Justification.CENTER_ALIGN,
        leading: Leading.AUTO,
        paragraphShadingBottomOffset: "0p1",
        paragraphShadingColor: myDoc.swatches.itemByName("C=75 M=5 Y=100 K=0"),
        paragraphShadingOn: true,
        paragraphShadingTint: 100,
        paragraphShadingTopOffset: "0p5",
        paragraphShadingWidth: ParagraphShadingWidthEnum.COLUMN_WIDTH,
        pointSize: 14,
        spaceAfter: "0p7.5"
    };
    myDoc.paragraphStyles.add(paraProps);
}
marginNumberParaStyle = myDoc.paragraphStyles.item("Margin_number");

// If "Margin_number" object style doesn't exist, create it
if(myDoc.objectStyles.itemByName("Margin_number") == null) {
    var objProps = {
        name: "Margin_number",
        anchoredObjectSettings: {
            anchorPoint: AnchorPoint.BOTTOM_RIGHT_ANCHOR,
            anchorXoffset: "2p9",
            anchorYoffset: "-0p5",
            anchoredPosition: AnchorPosition.ANCHORED,
            horizontalReferencePoint: AnchoredRelativeTo.PAGE_MARGINS,
            spineRelative: true,
            verticalReferencePoint: AnchoredRelativeTo.PAGE_MARGINS
        },
        appliedParagraphStyle: marginNumberParaStyle,
        basedOn: myDoc.objectStyles.itemByName("[None]"),
        enableAnchoredObjectOptions: true,
        enableParagraphStyle: true,
        enableStroke: false,
        enableTextFrameAutoSizingOptions: true,
        enableTextFrameGeneralOptions: true,
        enableTransformAttributes: true,
        textFramePreferences: {
            autoSizingReferencePoint: AutoSizingReferenceEnum.BOTTOM_CENTER_POINT,
            autoSizingType: AutoSizingTypeEnum.HEIGHT_AND_WIDTH,
            minimumWidthForAutoSizing: "1p8",
            useMinimumWidthForAutoSizing: true,
            verticalJustification: VerticalJustification.BOTTOM_ALIGN
        }
    };
    myDoc.objectStyles.add(objProps);
}
var marginNumberObjStyle = myDoc.objectStyles.itemByName("Margin_number");

// Delete all text frames with "Margin_number" object style applied
app.findObjectPreferences.appliedObjectStyles = marginNumberObjStyle;
var objectList = myDoc.findObject();
if (objectList.length >0) {
    for (var i=objectList.length-1; i>=0; i--) {
        objectList[i].remove();
    }
    alert("Deleted all existing margin numbers.");
}

// Loop through pages
for (var i=0; i<myPages.length; i++) {
    myPage = myPages[i];
    var noteNumbers = null;

    // Loop through text frames
    myFrames = myPage.textFrames;
    for (var j=myFrames.length-1; j>=0; j--) {
        myFrame = myFrames[j];

        // Loop through paragraphs
        myParas = myFrame.paragraphs;
        for (var k=0; k<myParas.length; k++) {
            myPara = myParas[k];
            // Check if para has header style applied
            if (myPara.appliedParagraphStyle == headerStyle) {
                ip = myPara.insertionPoints[0];

                // Get paragraph's number and add it to noteNumbers string
                try {
                    noteNumber = myPara.numberingResultNumber.toString();
                    if(noteNumbers==null) {
                        noteNumbers = noteNumber;
                    }
                    else noteNumbers = noteNumbers.concat("\r" + noteNumber);
                }
                catch(err) {
                }
            }
        }
    }
    // Create text frame and add noteNumbers string
    if (noteNumbers != null) {
        myTextFrame = ip.textFrames.add();
        myTextFrame.appliedObjectStyle = marginNumberObjStyle;
        myTextFrame.contents = noteNumbers;
    }
}
alert ("Script complete");
}