Just to add since I am currently in the process of a 97+ swap, and a 5.3 swap.
I wanted to keep a 5 speed transmission in my MJ, there is a difference in the firewall for the 5 speed and automatic. It is just a couple of holes to drill out but it is not something that I thought about before. You would need to find a 5 speed clutch and brake assembly to make this work which is getting rare. The aluminum bracket is the same however so that is good.
You can see in the picture where the dimples are for the bolt holes, and also the punch out for the clutch engagement.