Errors and more, my first illustrator script

Question

First, I should mention that I started scripting for Photoshop about a month ago and have had some really motivating successes there. It led me to this one task we have that is just incredibly repetitive and boring in Illustrator that I want to script.
I haven't gotten all the pieces in here that I need so far, and any form of help would be greatly appreciated, whether just suggestion, or really whatever. I don't mind doing research and trying things out myself.
The purpose of this script is to open a template file we have on our network drive, ask for a folder with a collection of files (these are files provided to us that contain the info we need to make labels), place one, save with a specific name, and start over, placing the next file, till they are all on the template. We do this before we can create labels for our products. There are weeks when it has to be done 50+ times and that's pretty mind-numbing.
The steps I think I need are:
ask where the provided files are that need to be placed
open template file
make sure the folder chosen has the right type of stuff in it (PDFs)
place the first file at specified coordinates
embed the link
lock the embedded link
ask user to proof information on screen (ok to continue, cancel to stop and let user interact with file on their own) (95% of the time, there are no errors)
use the embedded link's name as the name of the file and save it to a specific network location
repeat until all the files in the chosen folder have been done
I've been lurking around here for a couple days, reading up on how Illustrator works with scripting and have broken off bits and pieces of different scripts to adapt for my purposes. So far, this is what I've come up with:
function getLabelRequests() {
     return Folder.selectDialog('Please select the folder containing label requests:', Folder('~/Desktop'));
     function placeLabelRequests(selectedFolder) {
          var myDoc;
          if (selectedFolder) {
          var fileRef = File("/Volumes/myNetworkLocation/myTemplateFile.ai")
          open(fileRef);
          myDoc = app.activeDocument;
          var firstImageLayer = true;
          var thisPlacedItem;
          // create document list from files in selected folder
          var fileList = selectedFolder.getFiles();
          for (var i = 0; i < fileList.length; i++) {
          // open each document in file list
          if (fileList[i] instanceof File) {
          // get the file name
          var fName = fileList[i].name;
          // check for supported file formats
          if( (fName.indexOf(".pdf") == -1)) {
               // skip unsupported formats
               continue;
               } else {
                    // Give the file the name of the image file
                    File.name = fName.substring(0, fName.indexOf(".") );
                    // Place the label request on the artboard
                    thisPlacedItem = myDoc.layers['Job Form'].placedItems.add();
                    thisPlacedItem.file = fileList[i];
                    thisPlacedItem.position = [15,-45];
                    thisPlacedItem.embed();
     if( firstImageLayer ) {
     // display error message
     alert("Sorry, but the designated folder does not contain any recognized image formats.\n\nPlease choose another folder.");
     myDoc.close();
     getLabelRequests (placeLabelRequests());
     else {
     // display error message
     alert("Rerun the script and choose a folder with label requests, if you please.");
// Start the script off
placeLabelRequests (getLabelRequests ());
So obviously there's no loop in there, which is one of my problems at this point. I know what each of these chunks of code do, but can't necessarily understand all the syntax. Particularly things like
for (var i = 0; i < fileList.length; i++) {
I know it's saying that the variable i is zero, and while the list of files is greater than i, do whatever that last bit means, but I don't really know why it works or how it was constructed originally.
I haven't specified the save either, which might be why I'm running another of my problems, but I don't know how to get the name of the link to be the name of the file when it's saved. I also haven't given it a confirm to let the user proof either.
Here's my list of problems:
Running the script returns the image format error, even though the folder selected contains PDFs (I suppose I don't need to confirm the files are PDFs, that could just be incumbent upon the user)
Running the script places all the files into one iteration of the template (this may be because I haven't gotten the save or the loop in there, but I think it has more to do with the function being set up the way it is)
Obviously, it doesn't save with the link name as the file name
I don't seem to be able to figure out how to lock the link after it's embedded.
I also wonder if there's a way to, rather than opening-placing-saving-closing-repeat, to open-place-save, delete-placenext-save, delete-placenext-save.
Phew, sorry for the short novel.
Here is a copy of the template … or not. Can I not embed files in the post that aren't images?
Here's a JPG of the AI file that I use as a template
This document has two layers in this order normally:
Artwork
Job Form
And here are the blocks I'm using as placement for the information we are provided. These are taking the place of the files that need to be placed, and again, were PDF files, but I'm uploading as JPGs because I either don't know what I'm doing, or you can't upoad those file types.

Answer 1

I worked around the place options for the PDF by adding in a function I found on this forum. It detects clipping masks and deletes them.
There's one line in here that doesn't do anything, and I'm figuring out if it needs to be changed. After the clipScan function runs, I'm telling Illustrator to place a variable at a specific position, but because clipScan modifies the variable, it no longer recognizes that group of page items as the variable. Temporarily, I've used the original place position to make sure the link sits right where I want it to, but I have to make sure that the files we are provided never look any different.
If they do, I'll need to asign a new variable and set the position after clipScan runs, I think. If it's necessary, I'll update with the fix, otherwise I think this is the final script.
#target Illustrator
app.userInteractionLevel = UserInteractionLevel.DONTDISPLAYALERTS;
function getLabelRequests() {
    return Folder.selectDialog('Please select the folder containing label requests:', Folder('~/Desktop'));
function placeLabelRequests(selectedFolder) {
    var myDoc;
    if (selectedFolder) {
        var fileRef = File("/Volumes/graphics/Standards/Job Forms/Label Job Form-5C.ai")
        var thisPlacedItem;
        // create document list from files in selected folder
        var fileList = selectedFolder.getFiles("*.pdf");
        for (var i = 0; i < fileList.length; i++) {
            // open each document in file list
            if (fileList[i] instanceof File) {
                //open job form
                open(fileRef);
                myDoc = app.activeDocument;
                // Place the label request on the artboard
                thisPlacedItem = myDoc.layers['Job Form'].placedItems.add();
                thisPlacedItem.file = fileList[i];
                thisPlacedItem.position = [-50,10];
                var myLinkName = myDoc.placedItems[0].file.name
                thisPlacedItem.locked=true
                thisPlacedItem.embed();
                var clippingCount = 0
                clipScan(myDoc)
                thisPlacedItem.position = [15,-45];//this is the line that isn't doing anything right now.
                redraw()               
                //make sure the placed job form has the correct information
                var proof = confirm ("Does the job form have the correct information?", true)//needs the redraw step above or nothing shows when the alert happens. Redraw forces Illustrator to display the actions performed so far.
                if (proof) {
                    IllustratorSaveOptions = new IllustratorSaveOptions()
                    IllustratorSaveOptions.compatibility.ILLUSTRATOR15 //some of our printers have yet to upgrade
                    var onPO = Folder ('/Volumes/graphics/ •••Drafts•••/ • Draft Labels/ •On PO')
                    var saveFile = File(onPO + '/' + myLinkName);
                    myDoc.saveAs (saveFile, IllustratorSaveOptions)
            else alert ('Make note of the file with an error. This file will not be saved.')
            app.activeDocument.close (SaveOptions.DONOTSAVECHANGES)
    else {
        // if user cancels action, display message
        alert("Rerun the script and choose a folder with label requests.");
// run the script
placeLabelRequests (getLabelRequests ());
//////////////////////////function to remove clipping paths from placed item, thanks to KennethWebb, Muppet Mark and CarlosCanto on the Adobe Illustrator Scripting forum.
function clipScan (container) {
    for (i=container.pathItems.length-1;i>=0;i--) {
var item = container.pathItems[i];
        if (item.clipping == true){ //screens for locked or hidden items (removed this after true:  && item.editable == true       so it no longer screens for locked or hidden items
            container.pathItems[i].remove();
            clippingCount++;