Doing the engine swap
 

I have the 96 GT with the weak heads and have been considering an engine swap to the stronger 99 and up motor. I was already told that everything should fit fine, however I am worried about wiring. Should all of the wiring match up as well? Is there anything that I should know before I go ahead and send for this motor. I just don't want any surprises that we don't know how to deal with the day we put this new motor in. I'm sure all of you understand. What do the pros have to say about this.
Thanx.