I'd go with the pointer, and set it using that. I've always used a narrow tip paint marker to mark the harmonic balance pulley.
Miss while driving could be a wide range of problems. Anything from ignition (wires, cap/rotor/plugs). At idle the
engine is under very little load. When placed under a load the electrical "kick" to fire the plugs changes. Any weakness would result in a 'skip' or 'miss'.
I'd disconnect the spout connector (that dumps the disty to stock setting for calibration) and set according to the emissions tag. It also wouldn't hurt to hook a vacuum gauge up to manifold vacuum and see what you get. 18-22 inches of vacuum, holding steady is good. If the needle does anything other then remain stable? It could point towards other issues.
S-