I know I said I wasn't doing a speedrun for Creature of Kapu Cave Speedrun, but I saw a lot of the game while doing the Everything Wrong With video for it. I figured to work on it at least a little more.
When you make the necklace for Big Island Mike, there are a few variations on the conversation. She mentions extra shells, if she picked some up, and she mentions multiple necklaces, if she made more than one. The fastest conversation is no extra shells, just one necklace. That's .6 seconds faster than the alternative. In that same conversation, it's 1.5 seconds faster to ask about Kane Okala, as opposed to saying you already know about him. It's about .5 seconds faster to tell Mr. Mapu that you need the key.
At Quigley's camp, it turns out you need to listen to the fourth diary entry, before you can open the trunk. You don't need to listen to it for more than a second, but you do need to listen to it. I also discovered you have to get everything out of the trunk, and you need to press the power button on the radio, before looking at the solar cells.
Once you do all that, you go to Dr. Craven. You solve his puzzle for solar cells. You put the solar cells in, and you call Quigley. Switch to Joe. You ask Big Island Mike about his "try it and trade it system", then ask him if he ever leaves. He gives you Ulua bait and tells you to fish for 6 Ulua. Go fishing, then give Big Island Mike the fish, so he can leave.
Once he leaves, you go into his room and find the map. The game automatically switches to Nancy. Go to Quigley, and she tells you to get the clipboard. Do that, then go back to Quigley. This starts the frass puzzle.
Pretty much everything, up to this point of the game, is linear. And, actually, doing the frass puzzle is pretty linear, too. At least, I suspect it is. Probably the only variation is deciding whether to go to Kapu Cave before or after fixing the microscope. That doesn't make much of a difference, for a speedrun.