For flags, you will need to edit:
Look at "merflg5.tga", "merpnt5.tga", "shipflg5.tga", "shippnt5.tga" and "frtflg5.tga". Those are the flag files for the "Revolutions" period, and include the American flags. Where the American flag goes in those files, that's where you'll need to put the Swedish flag in the files for earlier periods.
- merflg2.tga, merflg3.tga, merflg4.tga - merchant ship flags in "Spanish Main", "Golden Age of Piracy" and "Colonial Powers" respectively;
- merpnt2.tga, merpnt3.tga, merpnt4.tga - pennants for merchant ships
- shpflg2.tga, shpflg3.tga, shpflg4.tga - naval ship flags
- shppnt2.tga, shppnt3.tga, shppnt4.tga - naval pennants
- frtflg2.tga, frtflg3.tga, frtflg4.tga - flags used by forts
Look at "merflg5.tga", "merpnt5.tga", "shipflg5.tga", "shippnt5.tga" and "frtflg5.tga". Those are the flag files for the "Revolutions" period, and include the American flags. Where the American flag goes in those files, that's where you'll need to put the Swedish flag in the files for earlier periods.