I freaked out when my painters washed their equipment on my front lawn. By the time I saw them, the damage was done. But there really was no damage. I watched it and nothing happened. Still, that water based paint becomes a durable plastic coating when it dries, so what you are seeing could very well be their old paint.

I wish people would write in before they start these projects. Removing the 3 inches of soil was unnecessary. That was the most valuable part of your soil. All you need to do to improve the health of the soil is to replenish the soil microbes (if needed) and then feed them. Soil microbes can be replenished with a very thin layer of compost. Then can be fed with any organic fertilizer or animal feed. I would start with the animal feed, specifically alfalfa pellets (rabbit chow) at a rate of 10 pounds per 1,000 square feet. Apply that now and follow up in a month with more alfalfa pellets at a rate of 20 pounds per 1,000 square feet. I would skip the compost because most soils have at least some residual microbial population from which to grow once they are fed. If you have recently applied a fungicide or insecticide, then go ahead and use compost at a rate of 1 cubic yard per 1,000 square feet. You can apply the compost and alfalfa pellets the same day if you like.

Stop watering so much. If you have standing water for a day, that might not be too bad. But if you have standing water all the time for 3 days, you will kill much of the beneficial fungi in your soil and turn it into swamp style soil. It can still recover using compost and alfalfa but if you just don't flood it, then you won't have to go through the recovery process.

Where are you in Calif?
Are you planning to grow grass? If so, what kind?
Is your soil shady?
You said you had filtration problems. Does that mean the water did not penetrate when you water it? That's a different problem and what you are doing will not help.