4.6 sohc to 4.6 dohc questions

I have searched around and a lot of the post on here have links to other sites with info on this swap, but the sites don't work anymore, or the post didn't answer all my questions. My question is what all would you have to do to swap out a 4.6 sohc engine from a 99 gt for a 4.6 dohc engine from a 99 cobra. I'm going to help a friend do this swap, but we need to know what all needs to be done in order for it to work. Like do we need to use the ecu from the dohc will the tranny thats in his car bolt up to the dohc engine? Any info on this would help. Any write ups on this would be very helpful also.

Thanks