What steps would it take to hack an Xbox 360 controller to accept input from a computer program?
You can hack directly into the physical switches and buttons on the controller. Leave the controller core functionality remain and interface to the console in its standard way. This eliminates the need to do any reverse engineering or other hand waving funny business. 

From the standpoint of the computer that would be manipulating the hacked controller interface it becomes easy as 1's and 0's through an appropriate interface to simulate the switches and buttons states.