I am just trying to find a way to store what would equate to a "Master Key" to decrypt information that is stored within the MYSQL database. Any other suggestions would be extremely helpful.
Saintless. The fact that you are asking for other suggestions tells me that you aren't really understanding the problem.
If you are putting the decryption key on the server to decrypt the files, then you don't need to encrypt the files in the first place. Putting them above root is just as secure (and honestly, no kidding around, that is very secure - secure enough for most purposes).
Think of it this way: If I give a delivery man an encrypted letter... and I give him the decryption key so that they guy at the other end can decrypt the letter... then I really might as well not have encrypted the letter in the first place. (If Wild Bill captures the delivery man, he'll have both the encrypted letter and the decryption key!)
So my suggestion to you is just don't bother encrypting the file. Just put it above root and you will be very secure (seriously).
On the other hand, if you wish to trick your boss into thinking that you have taken the utmost care, then by all means, encrypt it with the strongest military grade encryption possible... and then put the decryption key right there on the same server with the decrypted files.
Please understand, I'm not saying, "Hey Saintless, your system is weak! You need to be ultra-super strong."
See, the only thing worse than having a weak system... is having a weak system when you think it's a strong system. Think of it: Imagine you lock your car in a really bad neighborhood and you trust your new Super-Whamo Security system to sound the alarm if someone steals the radio so you leave the car alone for an hour. But the bad guys know that the Super-Whamo can be defeated with a paperclip and a piece of chewing gum and they steal your radio in 8 seconds flat. If you had known how vulnerable you were, you wouldn't have left your car alone in that neighborhood but since you thought you were secure, you took a risk that you wouldn't have taken if you knew the facts about how vulnerable you really were.
So I'm not saying, "You need to be military-grade secure". I'm saying that the encryption you're adding is actually a bad thing because not only isn't it making you more secure - it's doing the opposite by making you think you're secure when you're not.