Welcome to the world of non-lurkers Justin, we're glad to have you here.
What you are proposing shouldn't be that difficult to do, however it will be a bit of work especially if you haven't done something like this before.
For the ducting you may have to end up making something yourself. I'm not aware of any whole house fans that are made to hook up to ducting. In fact, most of them are just designed to pull air out of your house and into the attic, not blow into the house. I'm not sure how much benefit the ducting provides, but you may not even need it.
Another thing to think about is a whole house fan requires something to suck air through. Yes, there is the opening for the fan, but a window or something else must be open to suck air through too. How do you plan on automating this? I have seen guys use electronic actuators to open and close windows automatically so it can be done.
The arduino is an excellent selection for making a controller for this project. I currently have an use one for basically the reverse of what you're doing (I use mine to blow hot attic air down into my house for heating during spring/fall). I documented my project
here. You should very easily be able to use my exact setup and just a little reprogramming for your needs.