I don’t like the idea of just playing the game and let things flow based on my ignorant choices, we already had to go back a save when we learned the consequences of not saving an NPC so now I have that fear of ignorant choices impacting how the game plays out. So looking at the remaining quests we have and wanting to get them right, I am spending so much time Googling that it causes me to pause and consider stopping.
See, I think this is where you're going the wrong way. Of course, objectively, there is nothing wrong with playing like this.
BUT!
If you ask me, BG 3 is the kind of game you actually should let flow and not use a guide to go through it. I've been enjoying it so much (almost 240 hours worth of enjoyment since launch) specifically because I can have 3-4 playthroughs at the same time and, chances are, they'll be at least slightly different.
I've gotten to act 3 by myself, and I've also gone and finished the game with a couple friends, and lemme tell ya, those were two different experiences. I didn't use a walkthrough in mine, and while one of my buddies linked us to a doc showing where every weapon is and how you can find it, we only just skimmed it once and relied on a) what we already knew from our separate runs, and b) what we felt was right/cool/fun, so we can see where the story goes.
And I can say, personally, that if you let the story flow, let yourselves get immersed and try to roleplay a bit too, it gets very, very fun. For myself, if I start a new run, I'll not only create my custom character but, during the creation screen I also come up with a personality and a bit of a backstory for him, and take it from there as I play. This is actually why I wanna play a chaotic good Dark Urge next, for example, simply because the roleplaying potential seems really, really cool.
am I overthinking and should just play knowing I’ll miss new gear from puzzles, will miss quests and may not like the outcomes? Are we missing simple clues about the proper order to quests and treasures or are we expected to have to do lots of research to get it ‘right’?
Anyway, I got a bit long winded there, but for the tl;dr: you're not at all expected to do it "right". There is no actual "right", I think. Just relax, have fun, and immerse yourself in the game. That's also kind of the whole point of D&D, at least as far as I see it; you can min-max and crunch the numbers and so on, but the game is supposed to be an adventure (with some math), not just a math class so you can get progressively higher numbers.