Help Needed to get website running again.

PLEASE DO NOT APPLY UNLESS YOU UNDERSTAND WHAT WE NEED AND YOU HAVE THE EXPERIENCE TO FIX IT. We have a licensed copy of Boonex loaded onto an EC2 server running Debian and webmin. The website was live, although we experienced some file permissions problems which were preventing us from getting our extra modules from working (standard Boonex modules). We asked Boonex support and they advised file permissions were the problem, for which we had assumed was the original problem. Through the task of updating the relevant file permissions, we have found that now the web site is no longer active and it is saying "It seems to be script is not installed." We need an expert troubleshooter who can get to the bottom of the issue pronto and a) get the site back up and running, and b) Get all of the modules which have been installed running also. We will pay an initial milestone to begin, releasable when the website is running again; and a second milestone released when all of the modules (I think theres about 12-15 modules to get working) are working. Thanks.