1. Right now I'm currently in my third year of college shooting for a BS in computer science. But the school only really has one quarter of "internet security". I need more than that.
A college degree is almost crucial these days in my opinion. Even if you dont learn anything a degree says that you have the ability to complete 4 years of college which is no small feat in my opinion. Unfourtunatly you are right, most schools dont teach any thing cutting edge but its a great place to learn the fundamentals.
2. I know just for the heck of it I will shoot for a few certifications. I know some of you probably don't believe I need them and that's fine. But for those who do have some certs, what do you recommend?
No matter what anyone says, certs matter. Human Resources is trained to look for certs. Network + and Security + and all that type of stuff. I say get them if you can.
3. What kind OS's for servers should I set up on a network? Obviously anything Windows, but I'm not quite sure what Linux OS's I should set up.
Most Linux servers in the real world are Red Hat. Cent OS is the community fork of red hat so learning on these would be the way to go. You could also study for the red hat cert which is well respected.
4. What kind of programs should I run on the servers? Web servers, mail servers, ftp, ssh... you name it. Any books on the subject of computer networks to setup would be greatly appreciated.
Try them all and learn how to configure them. Once you learn why they failed then you can learn how to break into them.
5. Right now I have a pretty extensive knowledge of network basics, particularly the OSI model, handshakes, the different types of packets and what's contained in the headers.
Good! Most people miss the basics because they want to jump right into the "cool" hacker stuff.
6. I also have a great deal of understanding of metasploit, sniffers, network scanners... My only real problem is a lack of knowledge of the things network administrators might screw up while setting up networks like forgetting to change admin passwords. That's what I am hoping to change.
I would highly recommend the following things:
1. Setting up a test LAN at home
2. Signing up for the Offensive-Security Classes
3. Learn a scripting or programing language
All the best hackers I know were network admins and programmers first. Those are the essential skills.