Oh boy. Valvetrain geometry issues.

The best way is to physically measure the clearance between the lifter plunger and the retainer ring or snap ring. That is what you are actually setting. If the intake is installed and you cannot measure the clearance directly, you must choose one of your procedures. If the pushrod still spins easily with two fingers, add another .005" or .010" to your measured length AND extra length for plunger preload. If the pushrod is tight and is hard to turn, do not add anything to your measured length except the extra amount for your desired preload.
There is a a few thousandths difference in length between a pushrod that easily spins and one that does not spin easily.