Great advise! I also have plenty of experience changing diff and trans. I ended up building two custom brackets that bolt to my floor jack. Having the car the right distance off the floor is critical as you mentioned and sitting
on big jackstands with a piece of wood or rubber placed on top also provides a little cushion to make everything sit nicely. Once the car is on jacks I test the solidness of the car by giving it a gentle push and pull.
The D 44 rear bracket bolts to the upper outside bolts were the camber arms attach and is shaped like a V with a plate welded to the bottom.
On the trans I use 2 of the bolts that hold the cases together on the bottom that are about 4 inches apart. With the transmission bracket the bolt that holds the bracket to the jack I
leave it a little bit loose. This looseness provides enough play that I can move the trans into position with enough variance to find that sweet spot to get the alignment needed to line up the imput shaft.
Once the trans in place and secure with the C beam I simply remove the 2 bolts and the bracket and reinstall the bolts.
Yes... Nessisity is the Mother of Invention!
As far as remembering where all the bolts go when installing everything I like to create a rough drawn cardboard template with the holes for the bolts in the specific location as they appear. Its simple and easy to do and
makes keeping different assemblies separate from each other easy.