Alrighty then, I think I'm done. I have:
1) Deleted all the duplicates I could find.
2) reorganized and renamed the main folder's images
3) Collected and added a bunch of captioned stories to specific images totalling at 40 single stories. Then there are the series: April's Stallian Milking Competition, Creamy Ranch (Which is now complete to my knowledge), Peach Story, Peach Cam Show, and Pony
Just overall, I've done my best to streamline the collection and hopefully people will find it easier to navigate.
Here's the MEGA link:
Mega