While I was working on the quest at Helios, Old Lady Gibson and her dogs randomly attacked me. I hadn't saved in a while so I wasn't able to go back and prevent this... But Boone killed her and the dogs... So... How do I finish ED-E's quest? I really want the upgrades (I spoke to the FOA scientist at Helios One and he unlocked the first message that explains where ED-E came from... Where do I go from here?)

There are various places, she was only one possibility. Just keep him with you and you'll eventually get it.