Not sure, but it should be a pretty easy swap. I don't even think the computer would have to be changed. You could reuse the 99's tranny, but the flywheel would have to be changed out. I think that's about it.
What are you planning to swap? Motors? Drive shafts? Transmissions? Cars?
Your platform is the same. I don't see any problem in changing over anything. You just have to use the other parts that work with the part you are switching, like changing drive shafts, etc, when you switch transmissions.
I would assume that you are swapping '03 stuff onto your '99? Other than seats, I would leave everything else alone on the interior. You have a much better audio selection with the '99. I am modifying my '03 dash so it can take the audio components like my '99 has. The '03 six disc changer basically blows. The Eclipse CD player and separate six disc changer in the '99 totally smoke it.
I give up, why would you WANT to bolt up a 99 tranny to an '03 engine? The T-3650 isnt rated to handle the SC engines HP and will blow. Plus the fact that the T-56 is a 6 speed and worth every penny. You would be asking for trouble swapping out the engine without the transmission (and the other parts like cross member and drive shaft). My opinion.