Maybe I'll take on the easy ones first:
1) Forest got completely mind-blanked by the skulls, they hit him with a powerful possession spell, so he is now either dead or one of their zombie-like servants. Ed Greenwood actually modeled sections and ideas of Waterdeep around the city of Lankhmar from the classic fantasy series (Fafrd and the Grey Mouser). There were skulls under that city, and Ed put his own spin on his skulls, making them somewhat like Demi-Liches.
2) There are about 5-6 dragons in the top 3-4 levels of Undermountain. I put that old red dragon in an unmarked section of the dungeon. I also had a tie in with the Cult of the Dragon. Ed's first couple of novels that I read as a kid (Spellfire in particular) had lots about Dracoliches and the cult of the dragon. They are a kind of cult/church interested in creating more Dracoliches and also kind of worshiping them. They were trying to covert the big red dragon you met into a draco-lich, but as you could tell he was pretty confident in his power. I never rolled up what was in his horde, but probably hundreds of thousands of coins, magic items, and usually some interesting treasures (paintings, or sculptures).
3) That vampire that was involved in the fight with the skulls, was a random encounter. I read a line in the book that when the skulls show up sometime they just randomly target a bypasser, so when I rolled up what could be walking down the road and get pulled into the fight - I came up with a vampire, so I just gave him a bit of flair.
4) The artifact? You mean Glimbles staff? It was actually a piece of the tree of Yggdrasil (see here for more details -
https://en.wikipedia.org/wiki/Yggdrasil) the tree of life or worlds. There are several norse gods tied into the Forgotten Realms mythology, and I figured if you guys kept playing, I might set one of our higher level adventures in the outer-planes. The staff was nominally a staff of resurrection and healing which also had some additional powers related to each of the gods of Knowledge and Invention Ogham, Gond, Denier, and Millil. You would have been able to unlock some powers (mostly the resurrection ability) of the staff if you went to either the great library of the north or the Spirit Soaring church (highlighted in some of RA Salvatores novels). It couldn't be recharged but did have the ability to regenerate charges if in the right environment.
5) The Fat Man. He was actually based on an NPC detailed in the Undermountain Sourcebook. Ed Greenwood actually had him as an actual fat man, but I decided to make him an specialist wizard (focusing on enchantment and illusions) I decided he actually altered his appearance frequently to make it hard for his enemies to pin him down. In Ed's source book his name was something like Hethvelgi or something like that so I just gave him the name of "The Fat Man" and also had an "H" emblem that he used as his wizard mark in some of his spells and placed on many of his crates of goods. In Ed's sourcebook Hethvelgi was located on Level 1 of under mountain, and was involved in slave trading, and was also doubling as a silk trader in Waterdeep. I decided to locate him in Skullport instead to draw you guys lower into Undermountain. I gave him a keep, and lots of soldiers, and some higher levels employees. You guys killed most of them with your surprise fireball attack in the streets.
You guys rolled really well during your attack on the fat man's entourage and also had a really good plan for the attack. Then when Garl phased into the keep he was able to bypass a large amount of the Fat Man's defenses, and the rest of you were able to bypass nearly all his wards and get into his keep without setting off any traps or alarms. By going right into the keep you didn't deal with a lot of other potential problems. Then you guys took out like every guardian he had, and caught him by surprise in his inner circle. So I had him decide to flee with his greatest treasures (I was playing him as incredibly greedy - to a fault). Even when he attacked you guys in the forest, he was more focused on getting back his treasure vs. revenge. He needed that cash if he was going to reestablish his operation down below. Otherwise, he wasn't really going to have much left, so he mounted an ill attempt to take back his money... which failed and ended with him losing his head
I think I got the biggest of the remaining items...