When you launch eduke32 for the first time, the following screen appears:
As the instructions suggest, you are supposed to copy the "duke3d.grp" file to "/home/.eduke32/duke3d.grp" location, which is located on the internal memory. We symlink the $HOME directory location to the root of the filesystem, as seen when connected via FTP, so the path above will exist.
If the mentioned screen continues to appear after you have copied your data file, then $HOME/.eduke32/duke3d.grp file does not exist. Check if you have put it to the correct location.
I cannot answer the part of your question about Chocolate Doom, but the location you mention should be valid, assuming the wad is all lowercase. Run the "Chocolate Setup" to see if everything is correctly configured.
Are you sure your operating system doesn't hide file extensions, so when you attempt to rename them, you don't end up with "duke3d.grp.grp" and "doom.wad.wad"?