The Ultimate Guide

Follow the tutorial until you have spoken to the Bishop and grabbed the repair kits and tools from the Church's Chest.
Go to the west side of the Church and dig up the weeds until you run out of energy.
Go to sleep. Speak to the ghost and get the exhumation certificate. Go to the garden and read the sign. Go east to the tavern and speak to Horadric the Barman.

Ask Horadric about the burial certificate, the garden and the fresh meat, then trade the burial certification to him. He'll give you a letter for Krazwold the Blacksmith and 1.5 silver.

Speak to Ms Charm, she's the bint that loves herself that was singing when you entered. She'll not be there if you go to the tavern on the first day, this is why we didn't.

Speak to the nobhead in the tavern and ask him about the ink and paper and the Astrologer.
Miss Chain might try to talk to you. She's Horadric's wench and you can ignore that bltch.

Go south/east of the tavern to the Blacksmith and speak to Kreavold.
Give him the letter then ask him about metal ore so you get the furnace plans.
Sharpen the sword he gives you, then kill the slimes. If you're OCD about the slimes you can line them up so you can hit both with 1 swing. 2 swings to kill them both.
Speak to Krazwold and complete the quest.

Break the barrels and grab the loot in the following locations...
The house just west of the blacksmith, break the barrel and grab the Nails and Flitch.
The next house north for Scrap Metal and Flitch.
Back inside the Tavern for some more Scrap Metal and Flitch.

Speak to Horadric again to receive the Beer for Gerry.
Gerry stops you on the way home, tell him to do one.
Mine stone until you have 14 or run out of energy.
Go to sleep.

Chop down 2 trees and the 3 wooden bushes near the well.
Unlock Sawing and Firewood in the building technologies.
Build a Sawhorse.
Make wood billets a couple of times so you have 6 in total. (you might run out of energy)
Go to Sleep. Wake up when you hear the Donkey ring the bell.
Get the corpse and remove the flesh.
Exhume the body for the ghost quest (bottom/right grave)
Bury the new corpse in the hole, throw exhumed body in the river.
Tell Gerry to do one.
Sleep again until morning.
Finish billet if need be.
Go to the tavern and trade the burial certificate. Go to the blacksmith and buy 3 simple parts
Return home and build a Furnace. Build a Chopping Spot. Make 1 firewood.
Go to sleep, Make 1 Wood Billet on the Sawhorse. Make 1 Firewood on the Chopping Spot.
Fuel the Furance.
Go north and mine 1 Iron Ore Node, ignore the Slimes unless they come near you.
Start the Furnace to smelt the Iron Ore.
Go visit the Inquisitor on Witch Hill as Skull boy asked you nicely.
Grab the Iron Ingot back at your furnace and restart it smelting.
Unlock the Wooden Anvil technology.
Go to sleep. Grab the Iron Ingot from the furnace and restart it smelting.
Go down to the basement and watch Snake do his thing.
Smash the barrels. (if you're lucky you might get a simple part or some nails)
Have a little sleep to regain some energy.
Smash the last barrel in your basement. Grab the Iron Ingot from the furnace.
Make 1 firewood.
Go to Sleep. Grab the Corpse, remove the flesh and bury.
Sell the Burial Certificate.
Buy 4 Simple Iron Parts from the Blacksmith. (sell your rusty shovel if you don't have enough money) With whatever money you have left buy some Nails.
Return home and make another Wood Billet. Build a Wooden Anvil.
Chop down 1 Tree and mine 2 Stone Nodes.
Unlock Tool technology.
Go to sleep. Now we've done all the pre work during the first week, we'll be able to start the second week with new tools.
If you got lucky while smashing the barrels and found some simpleton parts or nails, you should able to make one new tool straight away, make an axe first.
Use your new axe to make more firewood and then start your furnace smelting your last piece of Iron Ore.
Turn 1 Iron Ingot into Simple Parts and make a new Pickaxe.
Go mine another Iron Ore Node while the furnace smelts, then start it smelting a 2nd piece.
Once you have 2 more Iron Ingots, make your new shovel.

Congratulations, you survived your first week, you got a completely new set of T2 tools while you were at it and you didn't have to use the wetstone to repair anything.

Go sell those old crappy tools to the blacksmith. Now you can celebrate by drinking Beer with Skull Boy in the Morgue.

Autopsies are probably one of the least understood areas of the game.

Use the Autopsy Table in the Morgue to remove Boby Parts from Corpses. Each Body Part has a different effect on the Red and White Skulls the Body arrives with and can be used later for crafting and completing quests.

The number of Red and White Skulls and the Corpse Decay with determine the Corpse Rating rating, which will impact the Graveyard Rating when buried.

Best Corpse Rating I've seen in the full release is 12.

White Skulls will increase the Graveyard Rating by 1.
Red & Green Skulls will reduce the Graveyard Rating by 1.

The maximum Gaveyard Rating a Corpse can have when buried is equal to the number of White Skulls it has with one exception. If a Corpse has no Red Skulls it will naturally get a +1 Graveyard Rating when buried.

• Flesh = Removes 1 Skull, starting with a Red Skull.
  
• Blood = Removes 1 Red Skull and adds 1 White Skull.
  
• Fat = Removes 1 Red Skull and adds 1 White Skull.
  
• Bone = Has no effect on either Red or White skulls. (Bug?)
  
• Skin = Removes 1 White Skull and adds 1 Red Skull.
  
• Skull = Adds 1 Red Skull.

The Brain, Heart and Intestine can remove up to 4 Skulls

• -3 Red & -1 White
  
• -1 Red & -3 White
  
• -2 Red & -2 White
  
• -1 Red & -1 White
  
• -2 Red or -2 White
  
• -1 Red or -1 White

The effects of removing the Brain, Heart and Intestine are selecdted randomly when the corpse is created by the game. Ideally you're looking for one of them to remove 2 Red skulls, but this might not always be possible.

One strategy is to sleep and save the game before butchering a corpse, so you can reload the game should mistakes be made.

A Good strategy after you have just opened the Church is to only remove the blood and fat, bury the corpse and dig it up later when you have the Surgeon skill unlocked.

When a Corpse gets dropped off by the Donkey, it's Decay Rating will be at about 99%. Should the Corpse be left and the Decay Rating drops to 90% it will gain 1 Green Decay Skull.

A Corpse left outside will Decay faster than one left inside the Morgue, a Corpse left inside the Morgue will decay faster than one left on a Morgue Slab.

After you have opened the Church you can manage when the Donkey brings a Corpse using the Box of Carrots. Placing 10 Carrots in the Box will get you 2 Corpses.

5 White & 2 Red

• Dark injection = +2 Red = 6 White & 4 Red
  
• Glue Injection = +1 White = 6 White & 4 Red
  
• Lye Injection = +1 White & +1 Red = 7 White & 5 Red
  
• Silver Injection = +1 White & -1 Red = 8 White & 4 Red
  
• Gold Injection = +2 White & -2 Red = 10 White & 2 Red
  
• Remove Blood = +1 White & -1 Red = 11 White & 1 Red
  
• Remove Fat = +1 White & -1 Red = 12 White & 0 Red

5 White & 3 Red

• Remove Skull = +1 Red = 6 White & 4 Red
  
• Glue Injection = +1 White = 6 White & 4 Red
  
• Lye Injection = +1 White & +1 Red = 7 White & 5 Red
  
• Silver Injection = +1 White & -1 Red = 8 White & 4 Red
  
• Gold Injection = +2 White & -2 Red = 10 White & 2 Red
  
• Remove Blood = +1 White & -1 Red = 11 White & 1 Red
  
• Remove Fat = +1 White & -1 Red = 12 White & 0 Red

5 White & 4 Red

• Glue Injection = +1 White = 6 White & 4 Red
  
• Lye Injection = +1 White & +1 Red = 7 White & 5 Red
  
• Silver Injection = +1 White & -1 Red = 8 White & 4 Red
  
• Gold Injection = +2 White & -2 Red = 10 White & 2 Red
  
• Remove Blood = +1 White & -1 Red = 11 White & 1 Red
  
• Remove Fat = +1 White & -1 Red = 12 White & 0 Red

Any 5 White corpses with more than 4 Red and you'll need to start removing organs. You can save scum and see what each will give or you can get the Cultist Perk to see what they'll give.

iirc you get the Cultist Perk when your relationship with the Inquisitor hits 75% (or completing the Snake quest line... can't remember which).

You'll need to start with 6 white Skulls to get a 12+1 (13) Graveyard Rating.

You’ll need 1 Red skull to use a Silver injection and 2 Red Skulls to use a Gold, or they don’t work.

Gold is pretty rare so I’d save those injects for a corpse you can make perfect with 12 White Skulls.

Researching an item in the Church basement shows its decomposition products. These are in the form of a powder, fluid, or extract. Each form requires a different machine to process it.

• Powder is processed by the Alchemy Mill and yields Powder.
  
• Fluid is processed by the Hand Mixer and yields Solution.
  
• Essence is processed by the Distillation Cube and yields Extract.

Items are processed in many ways, but an item can only have one element.
Currently, there are eight known elements that are matched in pairs.

• Health/Toxic
  
• Order/Chaos
  
• Acceleration/Slowness
  
• Life/Death.

Substances are processed in many ways, but a substance can only have one element.

Here is a world map from the alpha.