Sara, one thing, the well water is not oxgenated; that plus not running the fall may be a little too much risk all at once. As far as microbes, you can get a 6 pack of septic bacteria at Walmart. It is in the plumbing section and comes in a red foil bag with 6 packs inside. Mix with a bucket of warm water, let set for a while then pour in. Use 1 bag per week and see what happens.
One other thing, you dont want the water really clear if you want fish. They need the plankton, but I'm sure you knew that.
