To restore the site to MODX

Main page, when you click on the inner sections of the writes Not Found. Can htaccess problem, maybe with something else. Some time ago the site was hacked and malicious code inserted there. Perhaps I am wrong this code cleaned.

The terms of the project:
- MODX Revolution 2.6.1-pl
website hosting smartape
repository on networks, only today did the first commit, the previous developer just posted to the server and lost
- ftp access

Expected result:
- working transitions between pages
- find and, if you have to eliminate evil and malicious redirects
- help with deployment of project on server
- started changes to the repository

Deadline: evening of 3 April

In the response tell me about your experience with modx :)