@mitu I figured out why I ended up using Valerino's repository. I was trying to install gsplus to get a working emulator for the Apple IIgs. Are there any other emulators I could use (either from Retro-Pie Setup or Retro-Pie Extras) that could be installed as a replacement?

I backed up the RetroPie-Setup folder and deleted it. I tried re-installing the necessary cores packages to make it re-appear. At that point, I was able to update the RetroPie-Setup script to 4.8.9. I noticed that a few of my Spear of Destiny Files (Episodes 2 and 3) were missing, so I grabbed the GOG version of the game and compared the checksums again. After I added the appropriate files to the wolf3d folder, I tried reinstalling WolfSDL and it booted each of them up correctly.

Thanks for your suggestions and patience guys.