Update. I removed about 75% of the gravel, added more river bed sand, an amazon sword, Java fern and an anubias. I want to cover the background more in plants as the mud and foreground are covered, any advice? Also picking up some frogbit later.
Also upon the substrate change, my water has since become a little murky. I’d rather let nature do it’s thing and let it clear but is this normal at this point of the cycle?
Yes, cloudiness is normal. This is a bacterial bloom primarily. There are dissolved organics in the tap water (you would be surprised how "dirty" tap water is) and the bacteria that feed on these multiply rapidly, about every 20 minutes, since they have so much food available. It will clear naturally; I have had it take days, other times a few hours, I assume it depends upon the food source.