I can help you with all of the milestones, because you didn't name any of them, I'll just name the most difficult ones!
The Garden: Drag some people onto the strange patch below the cemetary, they'll water it if you have the Lake pizzle done!
Butterflies: Drag Goldenchild on Garden
Magic Plant: Drag Golden Child near the orange plant next to the lake. (I believe you need the Butterflies puzzle done to win this)
Treasure: Drag builder to beach and if it says "Is there something buried there" You need to keep picking em' up and dropping them there and eventually the'll start to dig. After a while, they will uncover treasuer.(Have 3 science and construction)
Cave: Automatically will happen after the golden childs born.
Fertillity Fish: Get a master farmer, and put it in the lake, eventually it will catch the fish!(Have 3 farming)
Cemetary: Drag a villager on the yellow patch of grass(Have two Spiritually)
Golden Child: Drag a villager to the Lake (Villager must be holding a baby, only one baby, Have 3 fertillity, and 3 spirtually, complete the Idol and ruins puzzle)
Idol: Drag a bulder to the rock (Have 3 Spiritually, and 3 construction)
Ruins: Drag a buider to the stones on the beach (Have 3 construction)
Hope this Helps! If I missed one you needed just add more information!

Yo can u tell me how to do al of em like u did b4? Cuz how you explained them wuz perfect.

Its all in here...

www.virtualvillagers3.net/tips/virtual-villagers