Good news! I have determined that the engine and transmission are the original to the car. I do not have the protect o plate to prove it but the Julian dates for the engine match up to be in the car. Before I got the car I was going by pictures and in the picture the car build date looks like an 03D and the engine is newer than that. Turns out that the picture was not clear because the build date is 06D and the engine fits perfect. Looks like the only thing that was ever changed was the turbo. It has a June date also but is not red and the turbo date should be older on a June car since the turbos were made in California and the cars built in Michigan.