Thank you very much for all the info.
My problem is that when I run "wadsmoosh.exe" it doesn't output a 'doom_complete.pk3' file at all... (I'm using Windows 10. I've run the .exe as admin.)
I've no clue how to check MD5 sums, and I don't really understand how to read the log deep enough so as to discover the issue, but that's ok, I'll eventually figure it out.
Edit: Fixed! I re-dl'ed Master Levels and used those fresh installs for WadSmoosh and it generated the 'doom_complete.pk3' as intended.
And the sky errors have been fixed as well!
Thanks again for the help!