I just re-downloaded it (on a new computer, too) and found the exact same thing happened. Here's the log again.
Not sure what to tell you, the boot.dol you provided is getting copied as main.dol successfully but WIT isn't seeing it. Is it possible you are running low on hard disc space and WIT is throwing the wrong error? Have you tried running this script on another computer or from a different storage drive?
@KhaderWelaye This is not relating to the script exactly, but I am making a script for a different purpose, and using JNUSTool works, but I want it to stop opening that GUI asking what files it should download. I pass it all the same parameters you do, the title ID and the title key, and it doesn't start downloading like it does for you, it opens a window asking me what files.
ALSO not sure what to tell you, have you specified the config file for JNUSTool correctly? If I were you I'd seek help here.