I can't explain all of your symptoms, but ... when you plug in an EHD, it sometimes happens that the drive letter is different than it was previously. So, if your lightroom was expecting the photos to be on the (for example) F: drive, and now your computer thinks this is the G: drive, then Lightroom considers the photos to be missing. A simple solution is to have Windows change the drive letter back to F: (you can find instructions on how to do this using your favorite search engine).
A better solution for the long-run is to assign some high drive letter to this drive, such as Y:. Then, Windows will not change the drive letter when you plug it in.
I am beyond frustrated. In trying to locate my photos (I thought I had finally "found" them) I merged folders because that was my only option. Now I can't find a.single.photo from 2014. I need some major help. I have tried to figure this out on my own by reading, etc and I am just creating a bigger mess.
OK, I think I found all but the original missing folder. Those pics, I believe, are in a folder that is now called "lightroom" as described above. I am not able to actually locate the individual files to make those question marks disappear or use the files, but I am wondering about something within that folder (when I find it in Explorer) called Lightroom 5 catalog.lrcat.lock that has appeared before and given me problems. Is this something I should delete? Will I then be able to put my files back where they belong?
That's not the problem. The problem is that your photos are not properly linked inside of Lightroom, and this can be fixed via these instructions: Adobe Lightroom - Find moved or missing files and folders
When you say you can't find certain items, are you searching using the Lightroom search features, specifically, do you use Lightroom to search for these photos by File Name (after clicking on All Photographs)?
If you can't find them in your operating system, are you searching using your operating system's search function?