Thanks for your help BetterRed, Watch4Folder didn't look like it would work for me, but it sent me on a google search path to which I found a piece of freeware called DropIt.
DropIt has a lot of love it seems, with various setup guides. I got it working!
Here is a nice guide:
http://www.online-tech-tips.com/comp...ime-intervals/
Here is what I did, in case others want to try:
First, install iOS 8 and GoodReader on your iPad, and iCloud for Windows or OSX on your computer, then install DropIt.
1: Right Click DropIt -> Manage Associations
2: Create a rule from D:\Calibre\*.pdf to perform a copy action to C:\Users\xxxx\iClouddrive\GoodReader\Books
3: Right Click DropIt -> Options -> Monitoring: Enable scan of monitored folders with Time Interval of 86400 (This can be anything you want, I wanted once a day). The Monitored folder is D:\Calibre
4: Back on the Main window under options, tick show progress window, tick start the process after loading, tick ignore unassociated files/folders (so it doesn't complain about what to do about everything besides PDF files), untick confirm for large loaded files.
5: Lastly, I manually copy my Magazines to C:\Users\xxxx\iCloudDrive\GoodReader\Magazines because I don't want to keep them in Calibre. I then use SyncBack Pro to backup that magazine folder as well as D:\Calibre to an external drive for safekeeping once a day.
A minor issue remaining is the way that Calibre truncates the filename of the PDF and appends the Author to the end. I would prefer to have longer book titles and no author info, and change all my existing files in my Calibre library to reflect that. Can anyone assist?
My major issue now is that Goodreader is only showing a grey adobe logo instead of the cover page for each PDF, unless you actually download the file onto the iPad. Google Drive actually displays the cover without you needing to download the file. As I said, the UI of GoodReader is what is currently the most annoying.
For annotations, I will just manually upload the copy that Goodreader makes, back into Calibre and send the email summary to myself and put it into Microsoft OneNote.
Finally, my problem is that my combined PDFs and Magazines are 4.73 GB, so I am pretty much at the limit for the free tier for iCloud. I will just cross my fingers that they will raise it to 10GB to compete with Google Drive and Onedrive, or pay to upgrade to 20GB in the meantime.