How tonstall the “Basic Server” Profile onto a “Minimal” Install of CentOS 6

The US National Security Agency (NSA) provides guides for hardening Linux and other operating systems which may be of some help. Since CentOS is so similar to RedHat, you may be intrested in:

• Guide to the Secure Configuration of Red Hat Enterprise Linux 5
  
• Hardening Tips for the Red Hat Enterprise Linux 5

There are a whole lot of questions here that you have, and not much information provided for us to go on. But, here are some attempts:

The first thing I'd check is to see if your PATH is getting set at all when logging in. To check that, login to the terminal and type echo $PATH. If the things you added are there, then great, on to the next problem. If they aren't there, then I'd verify you are actually running bash with echo $SHELL. If you are, can you check if ANYTHING in ~/.bashrc or ~/.bash_profile is getting set? I'd find something innocuous and change it, then logout and back in to see if it took effect (or just add something like FOO="bar";export FOO, then test it after login with echo $FOO). If your .bashrc and .bash_profile aren't getting run, I'd check to see if .profile is getting run, and then also check if /etc/profile and /etc/rc/bash.bashrc are there and are calling the user's profiles correctly.

If you find that things are actually getting into .bash_profile, then I'd check to make sure your script and the directory it is placed in has the appropriate permissions, is executable, and that the directory is actually in your path (maybe something else is setting the path variable after you set it and overwriting your changes?).

If none of that works, then please post the following here and maybe we'll be able to see something more:

env
echo $SHELL
echo $PATH
cat ~/.bashrc
cat ~/.profile
cat ~/bash_profile
cat /etc/profile
cat /etc/bash.bashrc