.005" is not good enough, you will generate wear and vibration. Gap on left, slide eng. to the right. Also hold trans side coupling while rotating the shaft coupling AND pressing forward "lapping" the couplings together, this will clean out any crud between the two. Also when checking a problem coupling measure, rotate 90 deg. re-measure, rotate 90Deg. re-measure, repeat to get 4 measurements or gaps, if the gap stays on the left, good, move the eng., if the gap moves each time you rotate the shaft you have a warped coupling. A warped coupling can be removed and a machine shop can "true" the coupling. Shafts that have not been aligned for years usually require some cleaning between the coupling halves with some sandpaper (320#)
Feel free to call with questions 985-542-4336