Nice write up! I resorted to some hints as I wanted to get the game finished in a short amount of calendar time but it’s also really fun to solve it all yourself; I _almost_ did that with Grim Fandango playing with my fiancee and it took seven years and still a couple of hints I had to look up!
I got stuck on exactly those two pixel hunting spots you mentioned. I got naturally caught by the goonies exactly once and I could’ve sworn it was mandatory and 100% scripted.
Nothing wrong with paper and pen, that’s what I used for the telephone puzzle and I enjoyed it. Taking pictures with the mobile phone is absolutely not cheating either, memory tests these games need not be!