The player's customized graphics are set up in player_setup_skelani_parts. (Lines 33-92 reads equipment, the part before that sets up the body customizations). If you want a static player appearance, you could change this script to just set everything to a hardcoded list of body parts instead of reading the player equiment data.
To remove the skeletal system for the player entirely, you just need to remove the skelani_draw_skeleton call in the Draw event and replace it with a standard sprite drawing function (e.g. draw_self), and then replace all skelani_set_animation calls in the various player state machine scripts with functions to change the sprite instead. (When you're done, you might also want to consider removing the skelani_init call in the Create event to save on resources)