The Wordof 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. Chuckie's evil/possessed look was added, along with Elaine's line about hoping Guybrush isn't the victim of a horrible Voodoo spell.
LeChuck may have arrived during those three days Guybrush spent hanging inside the pit.
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?
Assuming the whole game is All Just a Dream, Guybrush needed a Deus ex Machina to defeat his evil brother, so he simply pretended that a pair of prop skeletons were his parents. That, or LeChuck murdered them and hid their bodies there.
How did LeChuck get the materials for the Voodoo doll in LeChuck's Revenge anyways? We never see him get the materials for it.
Presumably, he has the "something of the dead" from Guybrush's parents. He states that the rest of his ingredients are flawed, as his doll only teleports Guybrush to the next room, as opposed to a dimension of pain.
For the thread he used the pink dress, for the body he used spit, and for the dead he used his parents. As for the head... well, maybe he used hair that fell off when Guybrush scratched his beard?
If LeChuck flew into the sky and exploded, how did Guybrush manage to find his beard? Why didn't Largo take the beard the first time he robbed Guybrush? And why didn't Guybrush use the Largo voodoo doll to get the beard back?
What's the deal with Wally's visual impairment? In Revenge, he only has a monocle on his left eye, and becomes blind upon losing it, but in Curse, he has an eyepatch on his left eye and can see just fine. If his right eye works perfectly, why didn't he just close his left eye in order to see better?
Why did LeChuck make a voodoo doll of Guybrush if he was going to drop him in a pool of acid?
Why didn't Elaine climb down the pit to help Guybrush, but instead just stood next to the hole, waiting for Guybrush to somehow climb back out after falling hundreds of meters, possibly into a pile of smashed rocks, and definitely into the hands of LeChuck? And how did she know LeChuck was down there anyway?