So basically i've installed every mod as they are intended and when i load into the story mode there are bears spawning in-air then falling from the sky, and then when i meet an npc they instantly become hostile and shoot me. Also a lot of npcs carry multiple guns, even the station clerks...

You might be running the LML examples that include some of these things to illustrate file modding. Double check your LML folder.

Problem solved, thank you so much!