I'm asking this because earlier the only way I had of unbugging a quest in the institute was to kill an npc (the next objective only showed up after I did this) so obviously I couldn't die and load back to neutral state. Now I need to go back for a quest and they instantly start shooting me. Is there any secret to this or am I screwed for this playthrough? lol.

mostly you are screw, if you are PC user it is likely you can use console to modify factions related thing, for the commands it is likely same as previous game (lot of previous games command still work in current game) but I think you will need to find a proper faction code to make this work

Ye I'm PC user. Any chance you could point me on where to find the commands / faction thing? I'm new to fallout

http://fallout.wikia.com/wiki/Gamebryo_console_commands

in old fallout there is setally, new vegas there is setreputation.

If their base code is remain the same, it is likely they are control by setally or setreputation. but either of them require knowing the faction ID which i am not familiar on how do they find this

thanks, so could someone provide me with the faction ID for institute? I'd greatly appreciated

maybe you have better chance to ask modding community but i guess they normally extract them with GECK and I am not sure is it available for fallout 4 yet