As you mention, 1, 3, 4, and 5 can all be handled via the Arduino. It is just a SMOP (small matter of programming).
I'm not sure if you are asking how to do have an Arduino fire off a camera, as it sounds like you may have that under control. But if you don't, as you mention, a shutter release has 3 wires: ground, focus, and shoot. You need to complete a circuit between the ground and focus to get the camera to do the 1/2 press of the shutter (normally focus), and then you need to connect all 3 wires to shoot. In some other cameras, you might not need to connect the focus wire as well as the ground and shoot wires to get it to fire, but in Olympus you do. If you don't want to do the 1/2 press shutter action, and just go to fire, you would solder the focus and shoot wires together. Now, it probably does not apply to your E-PL3, but on my E-5, when I was in live view mode, if I just connected the focus and shoot wires and made a circuit, it would sometimes give up on focusing if it couldn't achieve focus fast enough. So when I wanted to use a telegraph key to fire off my camera, I needed to have a longer period of time to focus before shooting, and I wrote an Arduino program for that (http://arduino.cc/forum/index.php/topic,117629.0.html). I used two opto-isolators between the Arduino and the camera. In terms of firing the camera multiple times, you would write the appropriate delays, etc. There are two commercial shutter releases with sensor and time based shooting that have their code available if you want to see how they did it (http://www.triggertrap.com and http://www.cameraaxe.com).
However, I tend to think the big part of the project is getting communication under water between your camera and you. Once you have some way of sending a signal, you can do the camera control. You could send a number of pulses for primitive control or send a character stream, and send a different byte for each control. There I can't help you.
As I mentioned in my last post, a minor second problem would seem to be fitting the Arduino in the case, and activating the shutter release, including the radio. I suspect that may be a harder challenge getting a small enough radio but one that has enough power to reach wherever you are. If you are tethering the unit (i.e. it is a ROV or some such), I could imagine using a fiber optic cable, that you put an Arduino controlling a light on one end, and a simple photo-resistor on the other, and use that to communicate to the Arduino in the housing (taping the fiber optic cable to the housing). There something like the IR libraries might be useful, since the IR controllers send multiple pulses to distinguish between the different keys of the controller, and different controllers.
instead of just 2 controls I may want to have 4.