I believe the "c" was more common in the cherokees, so it will need to be re-clocked in order to work in a YJ. And you might have a problem with the input gear since they were much more popular behind an auto than a manual trans.
re-clocking means to unbolt the input cone and moving it so that the drivers side of the t-case is up one bolt hole from where it is now. You will be able to see the difference if you take your t-case and set it with the new one side by side.
As far as the input gear, you should be able to use the one thats in your t-case, and since you will have the front of it apart anyway, its a simple swap, all you need is a good set of snap ring pliers.