From "Ships_init.c", Cutter2 has 12 guns of 6 lb, weight 100 tonnes, capacity 300, HP 1500, crew 54. PO_Hoy has 8 guns of 4 lb, weight 170 tonnes, capacity 1200, hp 800. Though perhaps smaller, Witch of Endor appears to be tougher and better armed. I'd therefore have Caroline for Midshipman and Witch of Endor for Junior Lieutenant.Does the even more tiny "Witch of Endor" need to be anywhere in there, you reckon?
As "Nk.c" stands at the moment, everybody gets HMS_Sophie. It's the default ship for Lieutenant in Napoleonic era.That does mean we lose the HMS_Sophie for Hornblower altogether, but that isn't so bad because I think she's still used for Aubrey and possibly Nelson too.
Indeed. I'm just not as certain what type of frigate is appropriate.Oh, absolutely! Which is why I don't at all care about having an Indy that doesn't look like the film one. I'd much rather have a proper frigate, which she is.

OK, Natividad is becoming more trouble than she's worth, so leave her for a future possible quest.Adding ships to the fleet is quite easy, but I'm not quite sure how to remove specific ships from your fleet again or how to replace them.
I'm sure it is possible, but there are a lot of variables to consider because of different player actions.
Commodore: Sutherland - Bellona
Rear Admiral: add Indefatigable as companion
Vice Admiral: add Phoebe as companion - Essex
Admiral: add Nonsuch as companion - RN_FirstRate
If you put Nonsuch into the first slot, replacing the player's current ship, it won't take long for someone to realise that a Vice Admiral can take some tiddler as a prize, swap ship to it, then claim his promotion to Admiral and have the tiddler replaced by the Nonsuch. So you may as well just add it as a companion and let the player decide which one to use as a flagship and what to dump so as to open up a slot for prize ships. By similar logic, if a Commodore can swap between ships then there's little point forcing anything into the player's own ship slot for any promotion beyond Commodore - just add companion ships.
My basic strategy would probably be to copy the entire British code to one of the other nations, replace all the rank names, then look through "Ships_init.c" for suitable ship replacements. Comment out exceptions for specific names, maybe pick suitable heroes for other nations to replace them.Would be much appreciated! I should be able to sort out the English Hornblower progression there as per your suggestions today.
But I'd really rather not do the same for all periods and all other nations too.