Sorry to hear about the gnats - I had no idea the larvae ate roots. That sucks.
I was reading somewhere that folks take the mosquito dunks and put them in a bucket of water and use that to water in to kill the larvae in the soil. Not sure if it works or not.
The vermi-compost we use when the bin is going there's a freaking swarm of those bastards this time of year every time we open the lid but I never get them the following year when I mix soil up. If we do very few.
Maybe going to take a little time for the critters and the prey to balance out. Once you get your gardens into full swing it will become a machine. Everything will take care of itself, cept for weeding but hey all part of the whole.
All your hard work will pay off. Keep up the good fight brother. Things change you can count on it.