Hang the boat in a travel lift with just one sling. Lift it off the trailer and move the sling until it lifts level. That is the boat CG. Start a couple of feet forward of the engine bay.

That's a good method. What do you consider the "sweet spot", centerline, ahead or behind the rear step ? Then, as drive box's may be added, aluminum cylinder heads replace iron, interior is changed and etc., do you use math to stay at the "sweet spot" or the sling ? Further, what is the simplest method to rig a bare hull. Some start with drive line length, but that seems crude. After everything is cut to length and bolted down it's a bitter pill to move things. A freight scale to weigh each component and math should save a lot of time and other resources. The finished project can be verified with the sling.

If you know the bare hull cg and where you want the target cg to be, then simple math and known weights will let you determine driveline length (along with proper fuel tank, batteries, trim pumps, oil tank, etc placement).

Sean, in your opinion, why do two or even more hulls from the same mold with the same components run and handle different from each other ? Is it anything obvious ? And, is the CG or prop shaft depth more critical ?

The human factor... I would say no two custom boats are identical (lay up/rigging/etc)

The cg and prop height are both critical, it would be hard to determine correct propshaft height without a boat that runs balanced. Also, remember there is a dynamic CG as the boat runs and the tunnel creates lift.