I don't think there's anything in the starting questbook which refers specifically to France. There's the one about life as a privateer which is fairly generic, and the one about "Turbulent Times" which just tells you that relations are varied. Which Ship's Log entries should I be looking for?
Looking through the list of side quests on the Wiki page:
. Girl won in a card game - shouldn't be a problem, random gambling followed by action on Martinique, which hasn't changed
. Artois Voysey - done, no problems encountered
. Baldewyn Coffier - done, everything happens on Martinique
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Cargo for Thomas O'Reilly - won't be for Thomas O'Reilly because his name will be different in Villa de Vega. Questbook will need to be made variable.
. Edgar Attwood - is this even possible unless you're playing Standard storyline?
. Elizabeth Shaw - needs to be disabled or seriously reworked because Antigua and Guadeloupe are disabled
. Vigila Mendes - done, no problems encountered, and you can give yourself a pat on the back for that one.
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Angelique Moulin's Father - as well as sorting out the reward, this would be better if Antoine Chamfort were altered. He's the only Frenchman in a Spanish fort.
. Missing Son of Spanish Admiral - done, no problems encountered
. Hard Labours of an Assassin - in progress, no problems expected, except English banker Geoffrey Bampfylde is maybe out of place in Portuguese Santa Ines
. Help the Boatswain - done, he hasn't changed and neither has Martinique
. Help the Church - already on your list
. Help the Lady - done, no problems encountered, action is on Nevis and Puerto Rico, names have changed but dialogs use variable names
. Help Turks Island Settlement - shouldn't be a problem, Turks is still pirate and Santo Domingo is still Spanish. (Was this moved somewhere else because Santo Domingo is not Spanish in later periods?)
. Rys Bloom - shouldn't be a problem, apart from an unemployed English sailor in what is now a Spanish port
. Nigel Blythe - never done this one so no idea what are the implications of "Early Explorers"
. Patric and the Idols - done, everything happens on Martinique
. Rescue Peter Blood's Crew - Cayman is now Spanish Las Tortugas so English Peter Blood may seem out of place, but he's a pirate anyway. Action is on Cuba, which has different island and town names. Should be OK if variable are used instead of hard-coded names
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Sabine Matton - Arnaud Matton's dialog needs a bit of work as it still refers to war with England and the French capture of <insert Speightstown name>.
. Saving Toff's daughter - done, no problem due to change of ownership of Kralendijk / Palo Brasil
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Search for Peter Blood's Ship - needs to be disabled or seriously reworked as it happens on Guadeloupe which is disabled
. Sink the pirate corvette - should be OK now that period-correct ships are used
. Sinking the Vogelstruijs - should be disabled as it makes no sense when Port Royale and Port au Prince are now Spanish Villa de la Vega and Santa Maria del Puerto
. Smuggling for Thomas O'Reilly - probably needs some work as it's not Thomas O'Reilly, someone else will need to try due to pre-requisite smuggling now
. Strange Things Going On in the Caribbean - Mefisto needs to be replaced with an appropriate ship type
. French Pirate in the Tavern - dialog needs work, you're not raiding English gold when Las Barbados is Portuguese
. Saga of the Blacque family - done, no problems caused by Jamaica now being Spanish, everything else happens on Martinique
. Silver Train - done, no problems if blank companions problem is fixed
. Thierry Bosquet - done, everything happens on Martinique
. Woman Who Lost Husband and Son - done, everything happens on Martinique
. Zaid Murro's Problems - done, everything happens on Puerto Rico
So, some dialogs need to be corrected, but the critical ones are "Elizabeth Shaw's Disappearance", "Angelique Moulin's Father", "Search for Peter Blood's Ship", "Sinking the Vogelstruijs" and "Strange Things Going On". Those are the ones which have more serious problems than slightly incongruous dialog. Alright, "Sinking the Vogelstruijs" is really only a dialog problem as well, but it's a big one. The change of ownership of various towns means that Spanish Santa Maria del Puerto is worried that Spain will attack Spanish Villa de la Vega, to which purpose a ship will smuggle explosives from Spanish Palo Brasil to Spanish Santo Domingo.