I just finished my CJ5 Project. I fitted a Dana44 in the front and a Dana60 in the rear. I moved my front diff forward by about 1' and rear rear diff out by about 3'.
The magic figure (I would say) would be to aim for the CJ7 wheel base. This will mean that the diffs sit at the extreme positions. This will mean that you can climb almost vertical walls.
If this is not what you're going for, you can always use your body as the measure.
I fitted a Chev 350 and moved the engine forward by about 3'. This eased the propshaft angle at the rear a little bit. I used a normal universal, but after using it offroad... I'll have to go for a double-journel propshaft. So save the effort and do it from the start.
If I would do your conversion, I'll use the gearshift position a reference and see where the enjine and transfer case goes. There are ways to solve cooling etc. if the enjine is a little bit to close to the radiator... (Read ... with many mods, anything is possible)
Here is a pic of my CJ5 from the side