How do I assess what to replace during repairs after a severe roof leak?
If not dried out building materials are an excellent food source for mold. I would not wait but remove the sheetrock and wet insulation now, a dehumidifier is a good idea but fans circulating air may be enough. I don't use bleach because it stinks for a long time. I use a 3% hydrogen peroxide and water mix, it doesn't stink and is just as effective at killing mold. Depending on the length of time it has been leaking it may be possible to save all the wood even the wood that has surface mold now by spraying with the hydrogen peroxide mixture. 

Most people don't know this but all wood contains mold spores at plywood plants the veneer is stacked after being pealed and within days the entire stacks are covered in mold. These are killed when the sheets get dried and the go through a second heating process when the sheets are glued together in Hot press. Dimensional lumber is sprayed with a fungicide as it is finished or it will turn before getting to the store and no one wants black lumber. 

So get the walls open and kill the mold assess the wood condition if the wood is solid just surface mold spray it. One place you may have to replace floor decking is if underlayment. Has swollen and started to break down, this would need to be replaced after the leak is repaired and the frame work is dry re insulate and put up new sheetrock. One thing I have suggested to my customers is with the walls open it might be a great time to add outlets if any might be wanted. Much cheaper to do it with open walls.