David it happens to us all! You get into an overthinking it mode. You have seen a bunch on your project now and for some reason we always think the worst. So good that the situation wasn't a situation! For the first time working extensively on this Jeep, you are doing great. I had to go back and retry, redo a bunch. I usually have that situation on every project.

The removal and reinstall of the Trans and Transfer Case Assembly is usually best accomplished as a unit. I have found it is much easier to remove and reinstall them as an assembled unit. With the Jeep high enough in the air, and a good rolling jack that has a good hold on everything, it is much easier to put the whole assembly up and in cross member and all.