That's an impressive little beast, especially at that price.
I had a quick Google and you just need to pulse the focus pin to GND (I'd expect 100ms would be a good). I'd suggest using a digital in, transistor out optocoupler between the microcontroller and the camera. That would be the minimum number of components to wire up while being pretty much bullet-proof in terms of camera safety.
It looks like Nikon use a variety of proprietary connectors so I'd buy a cheap shutter cable release to match the camera and then cut the cable off to get the connector and cable.
For your "keep alive" problem - Will a half press of the shutter do the same thing ? It would with a Canon so I'd expect the same with the Nikon. If that's the case, you could connect your microcontroller to the external shutter release connector and then you'd just need a transistor rather than an actuator and all the mechanics.
I agree about powering through the Ikelite strobe connector.
Since you mention using a microcontroller, does that mean you have the ability to get a custom pcb made ? I looked at doing something similar and was going to make my own PCB to go where the Ikelite one goes. That way you get the wiring to the strobe connector and power to your microcontroller and it's not rattling around in the box.
PCB's and microcontrollers are what I do, so it makes sense for me. It may or may not for you.
Maybe someone who has seen/handled this housing can answer this for me. Given the technical capability, would it be possible to make an adapter to fit a standard or modular dome port to this housing ?
This camera/housing seems to tick most of the boxes for me (especially with a mini-dome) except that I have a couple of over/under and snells window shots I'd like to try and get if the situation arises. It seems a bit silly to have both this and my existing 40D setup just in case. Any thoughts ?