Well, you definitely need a larger drive. I bought a 6TB drive through amazon and added it to my PC.
I use a couple of methods to keep track of my games. One is a folder system, with the main folders being New / Active / Updates / Completed / Failures. Then I have a folder for each game. I move the game to Updates when I have an update. I apply any mods that go with it and then add _ to the front of the name (
this serves to indicate not played yet). After I play it, I remove the _ and move it back to Active. Since the folders are on the same drive, it takes nothing to move.
But need some space. And since I have the space, I also archive a copy of whatever I download in case of errors, I can reinstall any version of the game with / without the mod / patch.
As for keeping track of updates I use
F95 Checker. It's a simple update checker for your games.