Secuirty Hippa ePhi Encryption

[eluser]Unknown[/eluser]
I have some down time and I am think of picking a new project for fun. I am a college student and every year we have a online pitch competition. I want to create a project for this pitch competition that is approx 9 months from now. The problem is the project requires very high security and the competition is a very competitive. I want to know if I can do the following with CI. I know that some if not all of these questions are not CI specific, but seeing as these questions are common to many of the CI programmers please don't dismiss them.

What I need to do
1. Store sensitive documents such as financial documents, .pdf|.jpg|.gif. Should I encrypt everything?
2. Three tier architecture. http://en.wikipedia.org/wiki/Multitier_architecture

Possible Solutions
1 I plan on storing all file in the DB. I know that there are many draw backs to doing this, but access control is the most important thing here. Also do I need to encrypt the files?

2. I assume I need to write two apps. One front app and a second middle app. The front app acts as an interface with the middle app which acts as an interface with Database. How Can I easy get the two apps to communicate with one another using CI?

Thanks for helping out novice.