I hope nobody will be offended if I just bring up a couple of discrepancies between the Vanished and Mysteries shows as well as as magazine articles.
In Vanished Ron says he went back to sleep after seeing Amy at 5:30 because he knew they were planning to get up in twenty minutes to have breakfast because they were planning to go into Curacao. In the other show he says he woke up at 6:00 but he doesn't know why, something just made him wake up. Vanished is the later show obviously so in effect there he claims to have known he was going to get up in 20 minutes and then does, in the earlier show he doesn't seem to be planning to get up but something, he doesn't know what wakes, him. In the earlier show he seems slightly annoyed when he asks Amy to turn off the light (a simulation) and when he insists that he would have shut the balcony door.
The times of when Amy arrives back to the cabin vary a lot. Some say 5 minutes after Brad. But one article says the ship lock system recorded I think 3:40 for Brad that article doesn't give a time for Amy but on Vanished Brad says she came back between 4:15 and 4:30. Lot's more time for Amy to be talking to someone alone though on the other hand they seemed to be separated for a lot of the night anyway.
I have no idea if these are significant differances or what it would mean if anything. Just documenting it.
One thing that struck me in the article: on the balcony Amy asks Brad if he has ever gone jet-skiing. Could this have been suggested as an activity to lure Amy? And this may be a little crazy but is there any way Amy could be jet-skiied from the boat? Overall, to her credit, Amy seems to have a bit more of any "edge" to her than the All American girl label would suggest I don't even think tattoos were as common as they are now back in 1998. Would she up for a pre-breakfast adventure assuming this is even possible.
I attach an article on how to jet ski with two people just in case this idea makes any sense.
http://www.ehow.com/how_2323457_jet-ski-two-people.html