After (re)setting the KOHA_CONF, we get:

failed: Access denied for user 'root'@'localhost' (using password: NO) at /usr/lib/perl5/5.8.8/C4/Context.pm line 411
Can't call method "do" on an undefined value at ./rebuild_nozebra.pl line 43.

There is a lot of other output too:

<yazgfs> isn't a variable assignment, skipping it<!-- [scheme:]host[:port][/databaseName] --> isn't a variable assignment, skipping it<!-- scheme: tcp, ssl, unix, http, sru --> isn't a variable assignment, skipping it<!-- can run all servers on tcp, but the unix socket is faster --> isn't a variable assignment, skipping it<listen id="biblioserver" >unix:/var/run/koha/zebradb/bibliosocket</listen> isn't a variable assignment, skipping it<listen id="authorityserver" >unix:/var/run/koha/zebradb/authoritysocket</listen> isn't a variable assignment, skipping it<!-- public server runs on tcp --> isn't a variable assignment, skipping it<!-- <listen id="publicserver" >tcp:@:9999</listen> --> isn't a variable assignment, skipping it

And do on and so on. It seems that the script understands nothing about koha-conf.xml. It just keeps repeating "isn't a variable assignment, skipping it" for every line in the configfile.