That the giant Monkey head is actually the head of an Humongous Mecha.
Presumably the title of the first game referred to the giant Monkey head leading to Hell, but the sequels did reveal more. (i.e. the tunnel to Dinky Island in MI2) -macroscopic
The Word of God is that it was originally just a dream. Guybrush ran off to play Pirates and Chuckie was sent after him. The whole thing took place in Not!Disneyland, hence the Treasure of Big Whoop being an E-Ticket (Disneyland used to use a graded ticket system with E-Tickets earning access to the most popular attractions). LucasArts wasn't satisfied with this because it ruled out further sequels, so the ending was changed. Chukie's evil/possessed look was added, along with Elaine's line about hoping Guybrush isn't the victim of a horrible Voodoo spell.
How did Guybrush's parents die? Or, if their skeletons are just part of LeChuck's spell, what did LeChuck want Guybrush to think? That his parents went to the lost property office, and then just sat there until they starved to death?