Well, if the tank sat empty for 3 days, you lost every bit of the beneficial bacteria that your filtration was holding. You have to have fish in the tank (unless you're doing a fishless cycle with ammonia) in order to keep the cycle.
So, basically, you're starting all over again. You overcleaned the tank and then by allowing the tank to sit without fish (even with established filter media) you had a die off of the beneficial bacteria. I'd monitor the water closely and do water changes as needed, probably daily. Feed minimally, since the tank may have to go through the full cycle again.
All that was really necessary was to treat the tank for ich with the fish still in it. :thumb:
If you hadn't added any new fish to introduce the ich, then another stressor in your tank must have caused it. Whether you see aggression or not, it can be a reality, and with this stocklist in that size tank, I don't see any way around it.
Where were these fish while the tank was sitting empty for those 3 days? Were they confined to an even smaller area?
It sounds like the johanni was injured, but it could also be a swim bladder issue from water quality/organ failure. (The body cavity of the fish will fill with fluid when the swim bladder is affected, and this will upset the equilibrium of the fish.)