I do it a little different than Mark. I do check with the bottom half only as the OP did, then install the cap and take a plastic mallet and tap the crank forward to get the halves even with one another. This is just to set the thrust then torque the cap down. If after doing this you still can't get what you want you can sand the thrust down by laying very fine wet or dry sand paper on glass or a surface plate and carefully sanding the thrust surface down.
I do check total movement back and forth like Mark has posted by prying.
Curtis