Good job for building this in CraftyMynes, I would have simply given up. When you mean it ain't working right, can you specify whether it's the clock, villager mechanics or golem spawning. Screenies may help, but I doubt it since the build is so huge and complex.

You can ignore iwarriiori. There is no official word on what is going to happen to the server 1.9, but it is very likely ONLY the nether and the end will be reset, but the overworld will stay as it is. Things may change over time, so don't take my words for sure.