I spent several hours reading/playing this story game today, making it all the way to the end of the preview version. The majority of that time was spent cycling back through that third day over and over, wondering where the missing clue was... only to realize (with the help of the "Heavenly Hints") that I had misinterpreted the one clue I thought I had deciphered!
From a writing perspective, there is not too much that I can say. Your grasp of the language is pretty firm, and the only punctuation/grammar issue I noticed on a repeated basis had to do with dialogue:
"Where did you get that key from, dad?" Your eldest queried.
Should be:
"Where did you get that key from, dad?" your eldest queried.
Otherwise, I encountered no coding issues.
Could the story be improved? Maybe, but this has to do with whether your intention is to write a story or a puzzle. And in what you label as "chapter 3," this very much becomes a puzzle.
As a story, I can see that you made very good use of your initial feedback, as the initial page did a better job at getting my attention as well as setting the stage for the recurring time loops. I still think the individual members of the family could be a bit more sharply drawn -- by which I don't mean the addition of oodles of exposition, but maybe three lines per person to describe what each family member means to me. This could be the brief remembrance of some little personality quirk, or perhaps a little anecdote of something the person did that illustrates that quirk. Otherwise, all I really pick up now is that there is a wife, two daughters, and a brother who chauffeurs everybody around. The women come close to being vivid characters, but the presence of the brother seems odd; did my wife and I lose our driver's licenses or something?
You seem to be a detail-oriented writer, noticing all the little nuances of daily life -- who made what for breakfast, and who prefers which brand of coffee, for example. I very much appreciate this, but it does make it stand out when some details get fudged.
One example is the reference to the baseball game on TV. I believe the time of day is 11:00 AM, and the game is already in the ninth inning. Elsewhere, a detail on the Philosophy Club poster leads me to believe the story is set in the month of October. The problem I had with this otherwise nice addition of detail is that professional, televised baseball games are never played that early in the day, unless there is a time zone discrepancy. In October, any game would be a playoff game, and none would begin until 1 PM Eastern Time. Given the average length of a baseball game is 3+ hours, that Giants game that is wrapping up at 11 AM would only make sense if the game was being played somewhere on the east coast... and this story was taking place in Hawaii.
Second, as I mentioned above, George's role in the story so far is... odd. Maybe his presence is explained in the unpublished part of the story. However, it would be highly unusual for a nuclear family of four -- where even the kids seem old enough to drive -- to be so dependent on the bachelor brother to drop them off at the seminar and then pick them up later. This detail had me asking questions that were never answered. Maybe there should be some salacious reason, revealed later in the story, why Mom and Dad can't drive anymore.
Finally, the seminar on physics, which seems to be such a key element of this first act, is glossed over a little bit too much in my opinion. Prof. Ratburn (interesting name!) steps onto the stage without introduction, asks a question, and then rapidly disappears. Liam seems to black out during the rest of that episode. And I find it hard to believe that no one would notice a cup of green goo placed at every seat.
A small number of choices seemed to be not in keeping with Liam's character. The one that really comes to mind is the "sneak around / pull a prank" option in the third chapter, which to me made sense only from a game perspective, and not because of anything intrinsic to the story. Liam, the character, is only vaguely aware that he's repeating the same horrible day over and over again, never retaining more than a slight sense of deja vu. The reader, however, is looking for ways to break the loop, so after a certain point I was playing more as Bill than as Liam, looking for keys and passwords. At one point, the entire family is breaking into a room, guessing a 5-character password, and obtaining a useful object. "The family that snoops together, loops together," I suppose. Later it's Liam doing the snooping on his own, even though he knows so little about what's happening to him at that point. I am pointing these out not as criticisms, but as places where the game elements are overpowering the story elements. Perhaps Liam needs to retain more memory between loops, so that he too realizes he needs to find the answers that are behind those locked doors.
As for the puzzles, I did ultimately need to cheat on both. The text one, I admit, was quite clever, and I did a virtual face-palm when I figured out where I went wrong. However, I think the clues for the numerical puzzle could be tweaked. One in particular was very abstract, and I'm not sure I ever would have gotten that one on my own.
Overall, I think you are on track to publish a stellar story-puzzle, or puzzle-story as the case may be. Not only are you seeking help and feedback, but you seem to be taking good advantage of that feedback. Having read your prior concerns about the on-page scripting, potential issues with the "go back" feature, and your use of items, I did have some reservations about what to expect.
However, now that I've read the story / played the game to the point where you have locked it down, I understand much better what you are trying to do. The "go back" button really isn't necessary, since there are no false endings to avoid. I expected the gray text to be distracting, but I learned that it was actually helpful in determining my progress through the loops. And the use of items works well here. None of it was buggy.
I am looking forward to reading more or the story! I just don't go changing the passwords on me.