Set the master password from terminal
First, a few things to note:

On the Mac the files /etc/passwd and /etc/master.passwd are only consulted when the Mac is booted into single user mode.

I'm not sure what you mean by "set the master password" for the Mac. Do you mean set the password for the account 'root'?

Usually you use the passwd command to change passwords from the command line (there is no master.passwd command) but you can't use it from a script as it requires input.

To change a password in a script you need to  use the dscl command.

Here is an example : 

dscl . -passwd /Users/tonyw newpass

Note that the above would have to be run as root, which means your script would have to be run by root. Otherwise you have to add authentication to the dscl command thus:

dscl . -u Admin -P adminpassword -passwd /Users/tonyw newpass

The user Admin must have administrator privileges for the Mac.

(All of this is incredibly insecure as you have passwords in plain text in a script.)

Of course to set the password for 'root' just change the tonyw to root in the above.

Have a good look at dscl(1) to understand the options in the above.