After you get the parameters and replace the board according to the service manual instructions (take lots of pictures with your phone, triple-check all connections before you power on), you need to install firmware, put parameters back, etc..
The service manual tells you, step by step, what do do after the board is physically replaced. For instance, if it says "update firmware," it will tell you where in the service manual the steps are for that. Is there a particular part of the instructions you're stuck on? I am not sure what you mean by "initialize the board."