I_B_I,
The main pond is about 6500 U.S. gallons. Plan on a main pump that will move at least that much water per hour. It should run continuously.
The upper pond is about 1600 U.S. gallons. The circuit you run on this will dictate the pump. Be aware of "head pressure" when dealing with lifting water.
If you are going to spill water from the upper to the lower pond then 150 gallons per inch of water fall width is a good place to start. ie. 12 inch wide waterfall needs 1800 gallons per hour.
Regarding your source water. Call your municipality and ask them what they put in the water. In the U.S. chlorine is a common water treatment and it must be neutralized.
Sodium thiosulfate is very inexpensive and very safe to use.
http://en.wikipedia.org/wiki/Sodium_...ate#Other_uses
With respect to solar heating, I am concerned that you will have difficulty maintaining a stable temperature for the koi. Koi need stability.
The raceway filter your are planning is a design that has been used in Japan for a long time. What type of media do you plan to use in it? Do you know anyone in your area that has this type of filtration? I ask because there is such a wide range of methods for filtration. The filter you have planned may be inexpensive to build however there are other designs that are much easier to clean.