I've had to re-do the pennant files as the ones you supplied had the old British pennants, not the ones I'd made with the reproportioned St. George's cross part.
Is there a way to make Swedish ships significantly rarer than everyone else's? There shouldn't be all that many of them as, realistically, there might have been the occasional trader, and maybe a warship up to frigate size to escort it. For that matter, "Ships_init.c" has no ships assigned to Sweden, so do Swedish ships appear at all? The obvious one to assign is the Swedish East Indiaman, though that's not available in "Spanish Main". Any of the Brandenburg ships ("Castel Friedrichsburg", "Brandenburg Frigate") might also be suitable, as they're also from the Baltic. If they can't be made to appear without them becoming as common as the normal inhabitants of the Caribbean then I'm inclined to put a toggle in "InternalSettings.h" to enable or disable Sweden, then anyone can choose whether to have them appear or not. The code which detects the flag could perhaps also check if the "Woodes Rogers" story is running and allow Swedish participation regardless, since the colony on Isla Mona gives their ships a reason to be present.