The partial data she found was indeed about the laser gun.
Here is a screenshot showing how they were improving the energy reactor and deciding it would work for guns.. and you finding that special energy weapon right next to the terminal this info is on. Also notice the mention it wouldn't be useful on the large-scale, like something the Institute wanted. http://i.imgur.com/6CI6rLi.png
Basically, a bunch of people ended up dying because the Institute couldn't have been bothered to actually fully investigate something considered important to them.
There's no proof Father-as-Shaun isn't a hoax either. All you have is the Institute's word and when you first meet them and after everything you heard, why would you trust what they tell you?
Deacon even cautions about comparing deeds with words about all the various groups that want you to join.
If you talk to the guy who created the gorillas, you find out that their aggression was actually not something that was intended. Within his terminal you'll find plans about how he wanted to create some sort of underwater synthetic realm and such. He was basically creating things at a whim--a whim he realized and thus said participation in his synthetic animal project wasn't mandatory.
You get access to terminals with deleted information, notices of your arrival, to hide info, to be on best behavior, and plans for things you could have already figured out for yourself in the Commonwealth. And the FEV lab, while not very well hidden was guarded by a robot that seemed pretty intent on killing anything that entered. It's like getting a tour from a local business; what you see has already been set up to be seen for you, being led along by somebody else's plan, and if you try to see something you shouldn't you tend to have to pay dearly for it.
Like Father suddenly deciding to release you from cryo to see what you did afterwords, setting up a confrontation with Kellogg that he knew you had a low chance of winning, of spying on you, of introducing a synth child that you were supposed to initially believe was your real son. If all that was, was just to test a synth kid, why not inform you before starting such a test? It's like you were barely more than an opportunity to test things out on. If he actually deep down cared and wanted to know about his real parent, then why use you like a lab rat?
Exactly, why would they pay more for my settler water when they have their own right there?