1.Do not research any building upgrades after refinery. Build x2 of each refinery and then upgrade in this order Farm>Eatery>Wells>Hospital BUT do not upgrade them back-to-back so you can still build wells, water pumps, eatery with regular materials.
2. Drop everything you are doing and pick up dead people and place them inside the cemetery. It seems the gravedigger can handle them better and also not get disease.
3. It looks like refinery buildings, forecast towers and sometimes stone huts wont let you pick them up. However, I noticed that if someone dies inside them it will not affect other nuggets.
4. Every time you join the game, click on your restoration god powers so you have it. If you are overwhelmed with repairs, hit PAUSE and CTRL-Click the buildings and then resume.
5. Hospital won't help you in disease outbreaks. Picking up diseased nuggets and killing them is the best way. Place anyone that is dead in the cemetery (other nuggets wont walk near or