Character customization data is defined in minit_title_charactercustomization (Script --> Menu System --> Menu Initialization). It uses the class data from init_player_classes (Scripts --> Data Mangling --> Player Stats), and the starting gift data is set up in the Create event of object obj_charactercustomization_setup. (The class data is used in some other places, like listing your class on the Status screen, but the starting gift data isn't, that's why the gifts are handled a bit less ceremoniously)
Damage is computed in rpg_compute_damage (Scripts --> Data Mangling --> RPG elements). It's a basic sum of ATK - DEF for all elements, the stats are set up by rpg_combat_statblock_init, and given actual values with rpg_setup_attack_stats for hitboxes. contact damage, etc., and rpg_setup_defense_stats for enemies.