The reason for the 8.8/9" is the pinion height on the 9" is 2.5" which means you can't get the input shaft under the diff with the 3.25" shaft centres of the top loader and the 8.8diff section is to fat so you have the same issue, combining the two solves that.
The 5 speed will be a different gear stack pacaged in the same main case with a different rear section to accommodate the extra length.
The 5 speed will be a different gear stack pacaged in the same main case with a different rear section to accommodate the extra length.