crossbred??? goldfish/koi fry are dieing

Question
I have a large outside pond 26' X 13' X 7'depth.  I stocked it with goldfish and koi.  Apparently someone has spawned and I ended up with hundreds of fry.  These babies are from 1" to 2 1/2" long, and vary in colour from black to a little orange to white - I'm not sure what to call them.  I transfered approx. 100 fry into a 55 gal tank in the house using just the pond water.  After 2 weeks I started to clean the water using an aquacleaner system.  There is also an airstone aerator.  I have been feeding them flakes, as well as the large pellets (which they seem to nibble on) and a little bloodworm.  Not sure what the eat.  Yesterday after about 3 weeks in the tank I found 6 dead fish in the morning and 11 in the evening.  This morning I found 8 dead fish.  I ran out and grabbed another 5 gallons of the pond water and put the filtration system on very low.  The water had started to clear so nicely we could actually see the babies.  There weren't any dead this evening.  Could you give an insight to my problem?  Oh, I had put a plant called hornroot (I think) into the aquarium as well - I was told this plant was fish friendly.  Any information would be appreciated.  Thanks!

Answer
It sounds like your problem is:

1)  There is too much ammonia in the aquarium water.  Ammonia comes from fish respiration and waste; as well from their food.

2)  The pH is too low.  This could be a result of excess acids, like Ammonia.

The water change would help in both cases by (1) reducing the concentration of NH3:H2O
                                            (2) reducing the concentration of H+:OH-

The solution would be:
1)  Incorporate some sort of biological filter into the aquarium as well as observe some other basic aquarium keeping practices.

2)  Test your water frequently until the Nitrogen cycle is complete.

3)  Reduce the amount you feed.  Only feed once a day; as much as the fish can eat in 2-3 minutes.

Be careful, long-term exposure to NH3 or low pH eats away at fishes' slime membrane.  The slime coat acts as a fish's immune system and once it's gone (only temporarily) the fish is susceptible to bacteria, parasites, and fungi.

It sounds like they are goldfish by the color variety you described.
I'm not sure what the aquacleaner is.
Once you test your parameters (pH, NH3/4, NO2, NO3, KH, Salinity) (or any of them that you can) let me know what they are and I can help you further.