I've been working on eradicating the too-wet soil, mold, mushrooms, and fungus gnat problems in my indoor garden for a couple of weeks now.
First I got rid of the seedling peat pots I had.... those had a combination of mold, mushrooms, and possibly gnat eggs in there.
Then I dried out the soil in all the plants. How my original overwatering issue got started was because I didn't realize that the soil in the root ball of the plants was very different from the soil I put the plants in (the soil mixture I used had better drainage than the soil in the root ball), meaning that even if the surrounding soil was dry, the root ball was still wet in a lot of cases. So... lesson learned on that point.
As I dried them out, I noticed that a few small mushrooms that had sprung up just died off by themselves.
Most of the plants were doing OK in terms of drying out properly, but I had to throw out one plastic planter that just wouldn't dry out, and had mold growing on the dirt (it looked like the plants were dying anyway). I think that got rid of a major place for the gnats to nest. The rest of the plants are in terra cotta pots... and I think I'm going to stick with terra cotta, since it creates much less of a retained-wetness problem.
After I got rid of the plastic planter, I haven't had any more mold problems or mushroom problems, and there hasn't been any visible fungus. Which is good.
I've been carefully monitoring the moisture condition of the root balls of the plants before I water now.
As for the gnats:
I did a soap flush (2 c. water, 1/2 tsp. neem oil, 1/2 tsp. Dr. Bronner's organic castile soap with tea tree oil in it) on all the plants. That seemed to dry things out further.
After that I watered all the plants with the cinnamon/chamomile tea mixture once.
During this time I've been putting fresh floral-scented soapy water traps for the gnats out about every other day. Right now I'm only catching 1 or 2 gnats in 2 days...which is good because it means there aren't many to catch. There are still a few flying around, but it's much reduced.
Also, I got some new light bulbs (10 x 30 watts of 5500K light) and new lamps for them where I can adjust the bulbs to be close to the plants, and the plants have really responded to the new light... they seem to all be improving. There's only one plant left right now that I am not sure if it will live or not... the rest of them are all showing marked improvement.
Embarking upon the world of indoor organic container gardening