Thanks for your feedback. It would be great if you (or anyone) can provide broken saves so that I can fix the mod. All the issues that I've been told about (since a very early version of the mod, which admittedly had an serious issue) have been a result of the game, not the mod. Where possible I add code into the mod to fix bugs in the game. The game itself is full of bugs, and the original walkthrough is carefully constructed to avoid the them. But if you accidentally or intentionally step of the narrow path defined by the walkthrough, you will very likely end up trapped in a loop. And if you don't use either the walkthrough or the mod, you're pretty much doomed to hours of misery, unaware that you're stuck in an endless loop. The mod helps avoid many of the bugs in the game, but clearly there are more that I've missed if you're still finding them.
The original walkthrough is nice if you don't mind flipping back and forth between it and the game at every step, but I find it difficult to remember where I was if I take a break from playing for a few days. Of course, I also have trouble remembering what day it is, so it may just be me.
You raise an excellent point about missing out on a lot by just following the green links. For those that do decide to use the mod, and want to see everything, I highly recommend clicking on all the yellow options before clicking on any of the green ones. The yellow options are ones that show content you haven't seen before. Sometimes they're just minor variants in the text (eg. "Hello, Bob" instead of "Hi, Bob"), but sometimes they contain a scene that isn't instrumental to the story but are nonetheless interesting (e.g. yoga by the pool). These are well-worth seeing, and you'll only have to see them once by following the yellow links.