So here's where things got really interesting. I guess you could say I found a work around, but it is weird and odd and doesn't make any sense. To answer your first questions, yep I could see all the documents and the folders in Finder, yes I had all full file extensions turned on, I was definitely using the same document folder.
So then what you told me at the end of your comment... Make a folder for myself through Finder. Did that, still didn't work. But here's the weird thing, I got really frustrated and started taking that folder and shoving it all over my computer. Screw it, what's the worst that could happen at this point. Well, I finally shoved it into the Library > User Folder..... what the hell, it recognized it. So I started throwing files into the User Folder, it can see all of those too. But the weird thing is, my Documents, Downloads, Applications, every folder I use on my computer are within that User Folder. Now as long as my hdc folder is on the very top level of that User Folder, HD recognizes it and uses it, but as soon as I put that hdc folder down into one of those sub folders, like Documents, it's off limits and blank and disappears. So there is definitely some kind of security flaw in my computer that I'm going to have to research on the Mac side of things and try and find out why all the folders within my User Folder are off limits to Java, but any folder added into the User Folder is readable and works.
Thank you to every one of you who have taken this long journey to help a poor player trying to recover all his old characters for gaming. I truly appreciate you all trying to help me out. Happy gaming to all and to all a good night.