There could be cross contamination between the backwash line for the softener and the soil line to the septic. I see a lot of guys who just shove the backwash line into the soil line with no air gap and the water system then becomes contaminated with ecoli.
Do you thoroughly chlorinate the entire house? Did you run every single faucet, shower, flush all the toilets, run the dishwasher, washing machine, outdoor spigots, ice maker in the fridge and the humidifier on the furnace? Is the a stubbed piece of pipe someplace that water doesn't run through? If you miss one water delivery when chlorinating, the bacteria colony will reproduce and contaminate the entire system all over.
There are no home testing kits for bacteria that I'm aware of.