How to I fix my site if it;s been attacked by a botnet successfully –

essentially my website goes down every night at the same time it appears

You need to start working your way through these resources:
https://codex.www.ads-software.com/FAQ_My_site_was_hacked
https://www.ads-software.com/support/topic/268083#post-1065779
https://smackdown.blogsblogsblogs.com/2008/06/24/how-to-completely-clean-your-hacked-wordpress-installation/
https://ottopress.com/2009/hacked-wordpress-backdoors/

Anything less will probably result in the hacker walking straight back into your site again.

Additional Resources:
Hardening WordPress
https://sitecheck.sucuri.net/scanner/
https://www.unmaskparasites.com/
https://blog.sucuri.net/2012/03/wordpress-understanding-its-true-vulnerability.html