I have tried to follow what you said 
 here  [www.hiawatha-webserver.org] but it just reinstalled Hiawatha with version 10.4, now my problem is that I cant figure out how I originally setup my custom configuration and how to point Hiawatha 10.4 to that new configuration.
Here is how my custom configuration is setup;
My directory tree looks like this;
/home/jack/server.conf/
├── apache2
└── hiawatha
    ├── etc
    │   ├── banning.conf
    │   ├── banning.conf~
    │   ├── bindings.conf
    │   ├── cgi.conf
    │   ├── cgi-wrapper.conf
    │   ├── cgi-wrapper.conf~
    │   ├── default.conf
    │   ├── default.conf~
    │   ├── directories.conf
    │   ├── directories.conf~
    │   ├── error.xslt
    │   ├── hiawatha.conf
    │   ├── hiawatha.conf~
    │   ├── hosts -> /etc/hosts
    │   ├── hosts~
    │   ├── index.xslt
    │   ├── mimetype.conf
    │   ├── php-fcgi.conf
    │   ├── php-fcgi.conf~
    │   ├── settings.conf
    │   ├── settings.conf~
    │   ├── toolkits.conf
    │   ├── toolkits.conf~
    │   ├── var.conf
    │   ├── var.conf~
    │   ├── vhosts.conf
    │   └── vhosts.conf~
    ├── lib
    │   └── hiawatha
    │       ├── libmbedcrypto.so -> libmbedcrypto.so.0
    │       ├── libmbedcrypto.so.0 -> libmbedcrypto.so.2.2.1
    │       ├── libmbedcrypto.so.2.2.1
    │       ├── libmbedtls.so -> libmbedtls.so.10
    │       ├── libmbedtls.so.10 -> libmbedtls.so.2.2.1
    │       ├── libmbedtls.so.2.2.1
    │       ├── libmbedx509.so -> libmbedx509.so.0
    │       ├── libmbedx509.so.0 -> libmbedx509.so.2.2.1
    │       └── libmbedx509.so.2.2.1
    ├── log
    │   ├── access.log
    │   ├── error.log
    │   ├── exploit.log
    │   ├── garbage.log
    │   ├── php-fcgi.log
    │   └── system.log
    ├── man
    │   └── man1
    │       ├── cgi-wrapper.1
    │       ├── hiawatha.1
    │       ├── ssi-cgi.1
    │       └── wigwam.1
    ├── run
    │   ├── hiawatha.pid
    │   └── php-fcgi.pid
    ├── sbin
    │   ├── cgi-wrapper
    │   ├── hiawatha
    │   ├── php-fcgi
    │   ├── ssi-cgi
    │   └── wigwam
    ├── site-file-hashes
    │   └── wp-filmod-hashes.txt
    ├── tmp [error opening dir]
    └── var
        └── www
14 directories, 54 files
My hiawatha.conf;
## Hiawatha main configuration file
# | I have seperated the files into .confs for easy seperate configuration of 
# | each file.
## VARIABLES
# | User defined variables
Include /home/jack/server.conf/hiawatha/etc/var.conf
## GENERAL SETTINGS
# | Hiawatha general settings
Include /home/jack/server.conf/hiawatha/etc/settings.conf
## BINDING SETTINGS
# Various binding settings
Include /home/jack/server.conf/hiawatha/etc/bindings.conf
## BANNING SETTINGS
# | Banning settings for misbehaviours
Include /home/jack/server.conf/hiawatha/etc/banning.conf
## COMMON GATEWAY INTERFACE (CGI) SETTINGS
# | CGI settings
Include /home/jack/server.conf/hiawatha/etc/cgi.conf
## URL TOOLKIT
# | Varioius toolkits such as banshee or monitor 
# | TODO - learn more on what I can do with toolkits
Include /home/jack/server.conf/hiawatha/etc/toolkits.conf
## DIRECTORY SETTINGS
# | To set various settings as per each directory listed
Include /home/jack/server.conf/hiawatha/etc/directories.conf
## DEFAULT WEBSITE
# | The default website for Hiawatha
Include /home/jack/server.conf/hiawatha/etc/default.conf
## VIRTUAL HOSTS
# | All the virtual hosts for this Hiawatha setup
Include /home/jack/server.conf/hiawatha/etc/vhosts.conf