Figuring out how the main puzzle works is a bit of an "aha!" moment, but it is easy to assume shoddy implementation if before that moment. In fact, everything seems to have been implemented quite well. It seems to me, though, that once one figures out what is going on, the solutions to everything else falls into place, so much so that it seems as though all the puzzles disappear.
I would have liked a little more story to this, however. While the premise is quite excellent, it could have gone a lot further: our hero should suspect that something is wrong the moment he lands inside the museum, not when he (apparently) discovers the chalice. In other words, there's not enough meat.
As a breakfast, this would be a one-egg cheese omelette and a small glass of tomato juice.