here you will find a small Wiki on how to obtain each ore or objective

Wiki:
To learn the procedures, the mod [​JEI] is recommended. The download link is this: [ Click here]

You can find muddy earth and other mud items at swampYou can find Dirty unknown ore in rivers, oceans and swampsYou can use bone flour to grow Muddy Rose but you can't make your flowers bloom so fastSapphire ores can be found in frozen rivers and oceansThe dark ruby ore can be found in dark forests or Roofed forestPink topaz ores can be found in the jungle biomesStar topaz ore can be found from the nether are used to polish and crystallize Topaz ores marwstar ores can be found in the nether and are used to polish and crystallize oresBy right clicking with the hoe in the main hand on the flowery Muddy Rose, you will get mud, the level of fortune applied to the hoe can change the amount of dropsYou can update your amulet by clicking it on a Carved mud stone altar, activating itTo upgrade you simply click on the lower level of the amulet and then add more of the crystal used to make itWith the altar activated at the basic level of dependence the ore used to make the amulet until the amulet is dropped at the Advanced levelWith the altar activated at the advanced level of dependency the ore used to make the amulet until the amulet is dropped at the Elite levelWith the altar activated at the Elite level of dependence the ore used to make the amulet until the amulet is dropped at the Ultimate levelWith the altar activated at the Ultimate level of dependence the ore used to make the amulet until the amulet is dropped at the Infinity levelTo create a mud-powered wooden farm is still under development