Cart, checkout, confirmation, thank you page and thank you email can only have one template each.
What is the customization based on? Each of those pages populates javascript variables with some of the order information. You might be able to use j-script to paint order-specific HTML. (If javascript is disabled in the browser your customizations won't display.)
Gonna write some JS to look for certain SKUs, set a flag and create some IF statements in the Cart to handle what I need. We shall see. I will post any positive results with code for others...