I've finished both It Came from the Desert games about a year ago using winUAE.. I never finished it on my real Amiga as I was too young to fully understand what I was supposed to do.
I agree they're really awesome games, I loved every minute of them. Some of my all time favourite games actually.
And you were right about using the numbers on that safe in the hospital basement.. it's just a lot of stress to use them properly. That thing operates just like a real safe and you need the game manual to see how to use it. Actually having the game manual helps a lot for many things.