You think it ended there? No fucking way. Because I finally managed to make the boys that play soccer on the school sports field appear. Yep, you read that right: when you go the field there's no fucking one there, so you have to perform a summoning ritual which involves you running like an idiot (because, let's be clear, you can increase your fitness by dancing in the school gym or running at the park, no need to run on the track field). Either that or they were just invisible and decided to make their presence known after you run a few times.
They are always¹ there after school. It is just that if the weather is shitty they do not play. The summoning ritual is simply to wait for a day without rain.
As for the rest of your troubles, they are a direct result of beelining a single (or a couple) of things while ignoring all others. Play in a weird way, and you risk weird results. Now, that is not a criticism; On the contrary, it is good to do things in a way not previously attempted, in order to expose weaknesses to be corrected.
Of course, some things are difficult to make resistant to unorthodox ways of playing. Take Mason approaching you because he has heard you are a Fixer, even though you have yet to go back to the Institute to become one. The alternative would be to lock off that conversation until you do go to the Institute. But then you would be wondering why those part of the Rachel story fail to progress.
Off the top of my head, I cannot see a smooth solution that would make sense under all circumstances.
¹ With one exception, but that cannot kick in until you know them well.
