So I removed all the rock surrounding the immediate area of the drain to repair it. Removed the rocks that were, by that time, all the way down into the drain itself. I added another base to the pipe protection, drilled more holes fro better flow, and put it all back together again.
Here is what it looked like:
This is the CF drain after removing all the rock and pipe
This was the original drain cover which was too small
This is the drain cover and pipe after adding a new base to the cover and drilling more holes
Everything is back together and before I put the rock back over the drain, I make sure everything is functioning properly.