#3. Aha! I'd found him there forever ago, but it was before I'd advanced Dan's quest to that point, so I'd completely forgotten that was something he was selling.
#2. Ah, okay, that makes more sense. I did a quick run-through of the map and the Goldspire was the other one I was thinking of, as well as returning to the swamp after the Eloin quest. Also, the Researcher's ID in Tomcallo was what I was thinking of as a keycard, as you find it after getting the notes about the observatory in the clinic. Totally understand cutting back scope when you're running the whole thing yourself, though!
#1. Didn't make the Delphine connection! I'd found the Accoro connection post-quest (the other two I'd found early) and figured that might have been part of it, but I wouldn't have guessed Delphine's relevance at all.
I did find the sword and shield! It's part of why I figured that conversation had greater relevance across the game, just wasn't sure if it also affected the order of events. Thanks again for all the help and insight!