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Given the ship fits in both Repair Shipyards, will a ship in Shipyard Repair mode repair faster at a port with a larger Port Size? For instance, would a ship repair faster at San Francisco than Alameda?

What I've read would indicate it does not. It also seems that the size of the shipyard does not matter except for the bigger shipyards begin able to possibly handle High and Critical priority easier.

Once the ship is in the Shipyard it uses only shipyard points for its repair. Size of port does not matter. Crew Experience does not matter. Captain's Naval skill does not matter.
Damage to the SY does matter. And I think the base with the SY needs to be in supply for the SY to do its work, but haven't seen it for certain.