You can see there are significant permissions or system issues.
Is that some kind of container? Is it normal to show 1000 as the owner/group? Usually not
And, even in the /etc/.../renewal/ folder each of the files shows a zero length. That's not right.
Something is preventing files from being written properly. Check your syslogs and whatnot. Whatever this problem is does not relate to your certificates or even trying to get them. It is a fundamental system problem.
Even try something like this and see if you can make a file
echo Test123 >/etc/letsencrypt/renewal/test.txt
See if it contains the string Test123. Try creating files in other directories.
Be sure to delete any file you manually create in the /etc/letsencrypt directories after a test
I do not plan to step you through debugging this. Just giving you ideas on how to begin that.
As for NPM, you can see it sets up its own cert names so you making your own cert won't properly integrate with NPM. Once you sort out the file system problem you will need to get NPM working or abandon it for some other solution.