Never made sake... don't know anything about it.
However...... you are not using enough water!
You said you are using 1/2 of this recipe:
and then you list your recipe as:
2.2 regular cups Millers Falls well water
5 cups (1cup-=5.2oz) rice
1.5 cups dried Koji malt rice (1cup-=5.2oz)
.5 teaspoon yeast
.5 lemon juice to kill germs
That link above says that it uses 0.9 gallon of water. So, by cutting it in half, you should be using 0.45 gallons of water.
2.2 cups of water is slightly more than 1 pint of water. In terms of gallons, this is only 0.14 gallons.
You only have 1/3 of the water you need (unless I made a mistake someplace.)