Glad you asked that and that you are aware of the procedure. You'd be surprised at the number of posts we get about moving data, after the new machine is up and running.
The best course of action here is to wait until the new Mac asks the question about transferring data from another Mac.
That way the new Mac is actually looking for the old one.
The procedure may take some time, depending on the amount of data being transferred but is worth the wait.
I am going to help a friend set up a new MacBook Pro and migrate data from a three year old iMac. He has the Firework 400 to 800 cable.
Question, do you start up the iMac in target mode after the migration assistant asks if you have another Mac or do it before you start the new MacBook Pro?