Keep in mind, all values are of type STRING.
To level up skills, search for the XP of the individual skill before and after a change. You may need to pin it at the value that you enter by checking the box, otherwise it will reset to a single-digit value. Some skills will level to 100 after reentering the menu once, while others you will have to repeatedly enter the menu while it levels up. More on this later, but if you want to mod health and energy, take care of those before you level the skills that are easy to level.
Easiest ways to get XP change to capture:
-Luck: Gamble at the tavern.
-Charisma: Visit the brothel
-Stealth: Drink with someone at the bar until you pass out and get robbed. Much easier than switching flags and sneaking around the map.
-Swords and firearms: go on a murder spree at the pirate village on the starting island. Exit and enter the village to avoid getting killed (eventually the town forgives you automatically)
-Cannons: Shoot cannons
-Accuracy: Hit stuff with cannons
-Defense: Receive damage
-Navigation: Not so consistent, but the higher the windspeed and sharper the turn, the faster the value goes up.
-Repair: Moor at an uninhabited beach, hit enter, and select repair.
-Boarding: board an enemy ship or two. No easy way around it.
Personal and Ship skill points can be searched and pinned after a couple level ups.
Modifying max health is straightforward, but max energy can only be increased by actually levelling up with the "Increasing Energy" perk. You can search the Rank XP and repeatedly level up to do it, but you want to search for your rank level and pin that at the same level so your rank doesn't go insanely high. Now that I mention it, all of this leveling up is going to send your rank through the roof, so beware the fact that you will immediately be encountering extremely difficult enemy ships that will possibly attempt to chase you down. Board as quickly as possible to avoid an extremely drawn out engagement until you get a class 3 or higher ship. With modified max health and maxed weapon skills you should be able to clear the ship even after your crew has been wiped out. Which leads to:
-Hull: can easily be found and pinned at max value
-Crew: easily found, but don't fill beyond 25% overload or you wont be able to fast travel, and I haven't found how to dump crew.
-Sails: no easy fix. Pinning it at 100% results in it constantly flickering back to the actual value while still showing damage, unlike hull.
-Capture and pin the crew value on the other ship and load your ship from there if you're having trouble doing it the other way around.
-Beware overfilling crew. If you go over more than the normally allowed 25% you won't be able to fast travel.
-All values can be found and modified fairly easily.
-I find it easier and more stable to modify values from a container and then load them from my inventory from there.
Things to keep in mind:
-Leveling up quickly means tough opponents before you may have the ship, crew size, and officers to handle it.
-Modding values causes major instability. Quicksave frequently (F6) but don't hit it if you're in the middle of a delicate operation, because you may have already moved some values beyond what are easily found.
-After modding anything, make sure that you tab out and uncheck the pin box. Seems to cut down on CTDs.
-The game is much more stable (less unstable) as you tab out if it is running in windowed mode. To access the config menu, go to the game folder in the Steam common folder and double click Config. ENGINE is the actual game.
Officer skills can be modded the same way as the player's skills, as long as they're slotted in the correct officer slot. To level their personal skills, you'll have to take them along as a boarder, and perhaps go on a murder spree at the pirate village on the back side of the starting island. Just be careful not to get them killed. The only worthwhile skills on the personal side of officers are the two that allow them to fill more than one slot simultaneously, so you can avoid the need by maxxing your charisma so that you can have more officers.