Can't Login as Root? (Centos 5)

Please take note that this steps were done in full caution, and with responsibility for anything terrible that could happen..

Last month, I was contacted by a client informing me that he/she cannot log in to the server as root for the past 2 weeks. Obviously they contacted me because I was the person responsible for setting up their server back in August. and, as far as I can remember, I never made changes to the server..

I tried logging in with all the passwords that I can remember, but to no avail.. I requested to work via TeamViewer to have a look at the machine.. yes its a virtual machine.. then I restarted the server..

Only then I notice that there was this error -> no user root found!

So I start googling and found this site:
https://wiki.archlinux.org/index.php/reset_root_password#Using_GRUB_to_invoke_bash

I followed most of the steps, but in the end I can't use the command passwd to change the password.. and the root user was not root.. apparently when I checked the passwd file, the line for root was nowhere to be seen.. seems like the passwd file has been modified...

DO THIS AT YOUR OWN COST!

So what I did was, I edited the passwd file on the line that I suspected used to be root - rename it to root again - based on the passwd file on other servers, and save the damn file..

Afterwards, I used the passwd command to change to root password (hey it worked!) and I exited bash.. an error message(?) or a warning(?) came up

Kernel panic - attempted to kill

But I crossed my fingers and reboot the server anyway.. and Alhamdulillah.. everything worked fine!!

NOTES:

If I was going to edit any files, I should have used/mounted a live cd/iso on the vm.. but at that moment, the damage has been done..

after this I'll try to use a live cd..