right behind the hub is right at the edge of the front bearing...should be .000 there...Must have been some crash to bend a crank that close the the bearing....
If you're checking it in a lathe chuck there is a problem, the crank is twisted in the center...you need to check it using a 1/2 or 3/4" steel block bored for a very close fit to the crank diameter ...Stick the tapered end of the crank through the block and indicat the end of the tape, it will most likely be .000...Indicat the other end of the crank without taking the crank out of the block..Any runout there is twist in the center..Block the web and correct the twist with a hammer...Slowly....
Try to get ,000, less that .002 should be ok...
a REALLY bad crash can bent the taper in the aluminum hub....
The stud can be perfect and will still show runout when tightened into the hub, it's the nature of the design...You can sometimes get the stud to .000 by gentle tapping when the whole thing is put back together...