But the .040 is taken by the lifter, not the valve.
Yes, pull the lifter apart and shim it, either all the way and figure .040 in later for length or shim .040 from max cup rise and extend the checking push rod to zero lash while on the base circle of cam and do it that way.
You get your push rod length when you add .040.... but in the meantime, you'll have the same lift with the lifter cup at full rise and no .040 figured in yet to the push rod zero lashed....again, because the lifter eats the .040 preload!