Sorry, I'm understanding your problem a bit better now.
You are correct in saying that the tip of the dizzy is not centred and will only go in one way
What I am saying is that if the flywheel mark is in the correct place, then No 1 piston should be at the top of its stroke. You can check this if you remove the spark plug. Maybe you can see it with a light, but I put in a small screwdriver to feel.
If the flywheel mark is correct, it might also be that No 4 cylinder is at the top. Thats why I said to rotate the flywheel one more revolution until No 1 is at the top
At this time, the rotor should point at No 1 lead on your dizzy cap. If it points at No 4, then your distributor is 180 degrees out.
You can see on the photo how the distributor fits to the gear. As you say, there is only one way for it to fit.
Perhaps the gear moved when you took out the distributor.
I removed the gear as well, it just pulls out with a strong magnet, and then positioned it the way I wanted so that the rotor faced the right way. When you put the gear back it turns because of the angle of the teeth. It turns about 20-30 degrees anti-clockwise.
