In studying a distributor, in which I also cutaway the cap, I think I know what your problem is.
Distributors have a significant end play in the shaft.
When the distributor is installed in the engine the gear rests against the top of the oil pump. This pushes the gear, shaft and rotor up quite a bit. I think that if you push the shaft up, or install the distributor you will find the rotor in line with the cap terminals.


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