I know that a few people have replaced the major city on the isle with the dwellers of the forbidden city. Which is a perfectly logical and evil thing to do. I do like the idea of placing the city down south between some of the villages. In the intro to dwellers, a Chieftain finds the PCs and tells them that trade has been hijacked by the denizens of the mysterious city. I like this because you can play off all of the villages. The PCs start in the main village of Tanora, they find out about some of the other villages and the trade issues. Maybe they've been expecting a shipment and the PCs catch wind of it and investigate.
The Lost City. It easy for the PCs to get lost and run out of food on the isle. The Pyramid doesn't have to be the typical Egyptian styled one, in the middle of the dessert. It could be a Mayan styled one, deep in the jungle. A fun intro could be that the PCs have wound up on shore after their boat sank, they have plodded along thru the jungle and finally stumbled upon the pyramid. Eventually maybe they will leave the pyramid and explore the Isle.
In Search Of The Unknown is a great dungeon that you can pretty much pop into any campaign. Having it reasonably close to the village of Tanora means that the PCs can investigate and make their way back to town often.
Keep On The Borderlands is another great adventure that you can pop into any campaign. My twist is a bit different however. One version is that the keep was built long ago and its location was lost in time. The keep is now overrun with Orcs, Goblins etc. Hiding in the caves nearby are Cavemen who have no memory of the keep. Alternatively the keep can be a forgotten outpost from the mainland, it manages to keep its head above water (jeez that was all kinds of puns there....) by trading with local pirates and some of the villagers. Cue usual kotb activities and the caves of chaos.
Horror on the hill is meant to be a self contained location north of a river, it could easily be popped onto the small island north of the isle of dread. To the east is a smaller island where you can put the town from the original adventure. Once again, this is a good spot for the PCs to wash up on shore, or possibly float by in a raft as they discover the rest of the isle of dread.
Another one that comes to mind is "rage of the rakasta"., which changes the way the Rakasta are in Isle of dread, but could setup some interesting stuff. A lot of the adventures from Thunderrift could be ported over to the isle.
In September I'll be running the Isle weekly. I'll be using Swords & Wizardry FMAG for rules. Should be lots of fun!
*This will be the second time that I've ran the Isle. I'm looking forward to it. Some of the above ideas may make their way into the adventure. Or may not.