Since no one knows what type of carriage was used on the San Francisco, we have to guess. The carriages below are from around that time period, and which deck the guns are on affected the size of the guns as well. I will probably choose the guns on the right for SF II.
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The old Model Ship Builder website used to have an article on the San Francisco, which I saved before the site went away. Here is an excerpt regarding the armament:
"The type of guns the San Francisco most likely carried is an interesting point. During the late sixteenth century naval armament production included the use of materials such as cast iron, brass, bronze, and wrought iron. Unlike many other European countries, Spain was still using predominately wrought iron guns on its ships. These were made of iron rods or strips that were held together with iron bands. If the San Francisco had brass (or bronze) guns it would have been quite modern by Spain’s standards and it would have been thanks to the investment of the Duke of Tuscany. In addition to the guns, the carriages that were likely used are of interest. A typical period British ship would have been using a fourwheeled carriage. This is because by the end of the 16th century many countries, such as England, were beginning to move away from boarding tactics to a focus on standing off and battering the enemy. Spain, which still considered using a broadside of heavy gunnery as a brief and preliminary action prior to boarding, was still using two wheeled carriages. These looked mildly similar to contemporary field artillery pieces and were difficult to aim and reload on a ship. But it is possible that if the Duke of Tuscany had invested in modern guns for the Florencia, he would have also insisted on four-wheeled carriages. Most sources note that the San Francisco carried 52 guns, this number would have included all armament from swivel guns to the largest cannon. Whatever type of guns the San Francisco originally carried, by the time she took part in the Armada 1588 she may not have possessed all of her original armament. This is because the Armada was so short of guns that it was ordered that they were to be taken from well-appointed vessels and redistributed throughout the Armada."
I have collected other information from research from other SF II builders and other sources if you are interested. One builder redesigned the hull, deck heights, and location of the wales to match a contemporary painting of a Spanish galleon which he hoped was a more accurate depiction than the design Artesania Latina used to make this model, and he modified his model extensively.
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