I had to go back to a very old saved game to find a quest id and fix a bugged quest. In the process I found the kid in the fridge and had a fun little quest. Is there a way to make sure you don't miss any quests? Do you look up quests online or do you make sure to check every square inch of Fallout 4?

And do you do all the side quests before finishing the main quest?

Of course you can find everything on the Internet...

You could also get the Vault Dwellers Survival Guide..it lists all side quests, main quests, and faction quests, also lists random encounters..I bought it a day after I got the game solely for better settlement help, but now on my second playthrough I peek at it every once in a while for some side quests..

The only side quests (that I'm aware of) that should be done before finishing the main story are faction related side quests..all others can be done before or after..

I didn't realize I should do all the faction related quests first before visiting the institute. Now I have missions from one faction that involve me killing members of a faction I joined. Do I just kill the members of the faction I joined? Will they know I defected?

I take your suggestion and use a guide to find all the side quests. I may have to play again to do all the faction quests.

I started wrapping up everyone elses after going to the institute. So far they havn't got mad at me for killing synths. Most synth patrols are friendly too unless I've killed a nearby courser. I remain prepared to go back a save when it comes to a head.