eh, it's a longshot and i'm no pro with php or shell but heres my idea.
1. googled a WHM account creator. so make a .php file with the following:
Create a WHM/cPanel Account | Mr PHP
edit it per needs of each domain. run the script via ssh. then repeat for all 50. guessing it'll take <1 hour max.
2. get files from nux, and extract OR use server-to-server FTP.
1. create a shell file with all of the domains in a list something like: (if you have a list, i'd say just use the replace method in notepad to make it work some how.) so you have a total of 50.
mv /var/www/<domain.com>/htdocs/ /eep/home/<cpanelname>/public_html/
2. zip up all of the contents in /eep/, or FTP server-to-server all of them into the /home/ dir.
my two cents, i don't really code much - but i see no reason why this wouldn't work.