Mostly in in settings.json in Starsector\starsector-core\data\config.
The variable for the fleet size limit is maxshipsinfleet, the variable for minimum combat zoom is mincombatzoom, and the variable for maximum combat zoom is maxcombatzoom; don't know if there's a separate variable for campaign zoom or not. If you want to make it more likely to recover your disabled ships after a battle, search for baseshiprepairchance; if you want to make it easier to board ships, search for boardingchance and boardingdifficulty. If you want to change maximum officer level, then search for officermaxlevel; if you want to have more officers, search for officerplayermax. If you want to change the fuel cost of going from point A to point B in hyperspace, search for unitsperlightyear, unless you'd really rather adjust fuel consumption by ship in shipdata.
Anything else?
