George -- I think Kevin has provided your clue. Measure the nose of the crankshaft from the "seat" to the end of the nose. Now measure the inside length of the pulley hub. That will give you an idea how much the pulley will stand proud of the end of the nose when the pulley is seated and nut is fully torqued.
And, you really don't know where the pulley will end up on the crank until it is actually torqued down by the pulley nut. Tapping with a rubber mallet probably won't get you there, at least it shouldn't. You should torque down the pulley, then remove the nut and observe how much the pulley is standing proud of the crank nose. A very thin film of grease on crank nose / pulley hole is ok.
As Kevin mentioned, "machining" the inside of the pulley hub is not a good idea. The fit is supposed to be a very tight wedge fit. So tight that a special crank pulley removal tool is usually required to remove a properly installed pulley.
Also as Kevin mentioned, alternator pulley alignment follows the fixed crank pulley, not the other way around. Install the crank pulley, then adjust the alternator / alternator pulley to line up.
Last note: Since this is a new rebuild it is a pretty safe bet that a previously installed sand seal shim washer is not on the nose of the crank . . . right?