Godarcher said:My question is if anybody happens to know if there is a script to manipulate faction relations
sure, it is the diplomacy related code, which defines the start of a new game relations and the events after it (when to declare wars, etc).
as you are not using Native modsys you will need to search for that code. Look for ID_scripts.py using things like diplomacy and war, like for Native "diplomacy_start_war_between_kingdoms" and "randomly_start_war_peace_new".
Keep looking until you find which code is used at game start (new game).