Oil pan, fuel pump, flexplate/flywheel thickness at the crank flange, alternator, and starter.  If you intend to run an original drive line, you will need the length plus that of the PTO.

You need to be set on your engine, i.e. Mark IV, Gen V, or Gen VI for example.  The crankshaft flange is a different length from the bell housing surface of the block and therefore affect drive line length.

If you are going to re-set the intake or particularly if doing a setback, do that first or at the same time.

If you intend to run a Jet-a-Way, you at least need one for mock up.  With a Jet-a-Way, and a rail kits that hasn't been intentionally setup with a Jet-a-Way, the Jet-a-Way shaft will be too high once installed.  You can, however, go the other way and mock up for a Jet-a-Way and simply install a longer drive shaft without issue.

Other compromises, such as interior, that affect engine placement should also be taken into consideration.