The Ghost Host's true identity as the Great MacGuffin is hinted at at the very beginning in the Stretching Room- a professional stage magician would be well-versed in making and using convincing secret escapes... which also helps get around the original ride's implications of the Ghost Host's suicide by hanging!
When the Hitchhiking Ghosts cameo in the end, they are portrayed using their 3D models from the updated Walt Disney World ride, rather than being portrayed as humans or Muppets. Most likely, this is due to the “sympathetic vibrations” being limited to the mansion, as the ghosts outside the mansion were portrayed as humans, rather than anyone Gonzo and Pepe personally knew.
When Gonzo and Pepe first enter the Mansion, they're taken to the famous Stretching room, complete with the iconic Stretching Portraits - portrayed completely accurately, except for Muppets replacing the characters. However, we only see three portraits, when the ride has four. The missing portrait? The elderly Constance Hatchaway. In this special, Constance is played by a human actress, not only making her the odd one out of the Stretching Portraits, but Foreshadowing her actual appearance. Pepe not seeing her portrait means he isn't warned how seriously Constance takes the phrase 'til death do us part' in the wedding vows.
During the wedding between Constance and Pepe, Uncle Deadly, as the officiant, remarks to Constance, "Sixth time's the charm! (aside) That's what Henry the Eighth said." The sixth wife of Henry VIII escaped him by outliving him - which is what Pepe (with considerable help from Gonzo) does too.
At the end, Gonzo and Pepe dash for the gate as the sun rises, lest they be trapped there forever- and the Caretaker makes no effort to follow them. He is already trapped on the grounds for all eternity.
At the beginning, we see the caretaker chiseling a pair of unmarked tombstones. When Gonzo and Pepe escape later, we see the finished tombstones were for them, under the assumption that they would fail like everyone else who had attempted the challenge. The caretaker knew who they were and why they were there. This, combined with the above detail, leads us to believe that he was a previous guest who took up the mansion’s challenge and failed.
The Haunted Mansion is said to house 999 spirits, but only so many of that number is featured in the special itself. Imagine the other spirits roaming about that we didn't see? Spirits resembling Clifford, Bean Bunny, Seymour the Elephant, Thog, Camilla, Link Hogthrob, Annie Sue, Dr. Strangepork, Mahna Mahna and the Snowths, the Sam and Friends cast, Wilkins and Wontkins, Taminella Grinderfall, even Skeeter!
