I am also having this problem when I try to login to a new SF3 server. I'm using the latest version of Skyfactory on both the client and the server, and I haven't changed any mods/configs. The items that are missing are apparently the Extra Utilities builder's wand and creative builder's wand, but both the client and the server are using the same version of extra utilities so I'm not sure how this is possible.
[11:47:14] [Netty Client IO #5/INFO]: Found a missing id from the world extrautils2:itemcreativebuilderswand
[11:47:14] [Netty Client IO #5/INFO]: Found a missing id from the world extrautils2:itembuilderswand
[11:47:14] [Netty Client IO #5/INFO]: Reset configs to client values for com.enderio.core.common.config.ConfigHandler
[11:47:14] [Netty Client IO #5/INFO]: CLIENT: Disconnected from server, enabling all click actions
[11:47:14] [Netty Client IO #5/INFO]: Loading configuration files
[11:47:14] [Netty Client IO #5/ERROR]: Failed to connect to server: there are 2 missing blocks and items