Be carful with the air system when first starting it up. I realize that your home-made system may or may not be moving the same amount of water that a store-bought system would, but you are supposed to bring those up gradually. If you just turn it on, you will likely be bringing up deep waters that are void of 02 and will also have toxins in them.
My GUESS is that you are losing some fish due to the stress associated with transferring them into the pond. And, you may have added to the stress by mixing up the pond waters. The fish go from one type of water/pond being jarred around in transit, all the while using up the 02 in the containers and soiling it with there urine and feces, then go into your pond waters. Temperature changes often occur during this process, then to add to it an aerator changes the water conditions(02 levels, temperature, biologics, and chemistry)yet again.
How deep is your aeration hose?
Did the aeration system cause a septic smell?
Are there any signs of illness on the fish (dead or alive)? (spots, fungus, white blotches, swollen gills, etc)
Did the aeration system cause a septic smell anytime after start-up?
Did you acclimate the fish slowly to get them used to the different water chemistry and temperature while stocking?
Answers to these questions will help the forum help you.
All I can suggest is the you keep a count on the dead fish so you know how many to replace and as far as the aeration is concerned..that's a toss-up. Did it do any harm? If so, is the worse behind you? I can't say for sure. If it is in shallow water then it's not a strong risk, but if it's in deep water (the lower 2/3rds or 1/2), it could be bringing up nasty waters and should be turned off and/or moved to the shallows.
