In addition to my comments above, not only do the files appear to be in the correct location and the /conf file accurate, but the directory permissions (/etc/letsencrypt/live/my-domain) seem correct to me as well:
lrwxrwxrwx 1 root root 46 Feb 9 11:37 cert.pem -> ../../archive/my-domain/cert2.pem
lrwxrwxrwx 1 root root 47 Feb 9 11:37 chain.pem -> ../../archive/my-domain/chain2.pem
lrwxrwxrwx 1 root root 51 Feb 9 11:37 fullchain.pem -> ../../archive/my-domain/fullchain2.pem
lrwxrwxrwx 1 root root 49 Feb 9 11:37 privkey.pem -> ../../archive/my-domain/privkey2.pem
Here's the perms on the /archive:
drwxr-xr-x 2 root root 4096 Feb 9 11:37 ./
drwx------ 3 root root 4096 Feb 9 00:56 ../
-rw-r--r-- 1 root root 1850 Feb 9 00:56 cert1.pem
-rw-r--r-- 1 root root 1850 Feb 9 11:37 cert2.pem
-rw-r--r-- 1 root root 1586 Feb 9 00:56 chain1.pem
-rw-r--r-- 1 root root 1586 Feb 9 11:37 chain2.pem
-rw-r--r-- 1 root root 3436 Feb 9 00:56 fullchain1.pem
-rw-r--r-- 1 root root 3436 Feb 9 11:37 fullchain2.pem
-rw------- 1 root root 1708 Feb 9 00:56 privkey1.pem
-rw------- 1 root root 1704 Feb 9 11:37 privkey2.pem