First to answer questions:

Just curious what tools will be needed for farming and can the special item the harvester be used?
New tools such as a hoe and trowel will be added. The harvester is a shovel which is currently used in place of a hoe for creating plowed land.

Has there been any thought as to our natural rainfall in the area watering plants for farming?
Yes, rainfall does actually increase your plants' water level, so you'll have to water less (or not at all) when it's raining often.

If you have to use guts as fertilizer, why can't you also use dead fish?
I've added fish as a fertilizer (see the forthcoming notes below).

I'm not understanding the 2 options either. Under option 1 Would raw foods produce zero calories and cooked food be the only method of calories
No, they will just provide less calories than a cooked meal, same as option 2.