Silly question....but-

The distributor cap has the cyl. #'s labelled on the plug wire terminals. Are the correct wires going to the respective terminals?

It's very easy to pull out and rotate the distributor back the 40 degrees -it should pull out when a single bolt (the one that you have to loosen to set timing) is removed. Quick and painless experiment worth trying....I think.

Does the missing improve much at higher rpm? I wonder if you have a lean miss, possibly made worse by the throttle position switch being out of adjustment so that the idle compensation at the ECU isn't working.