Im afraid you will need to start over. Use sterile soil-less seedling mix, do not add such additives as the alfalfa etc. young seedlings don't need it and I think I see here a combination of several problems but the most severe and irreparable is fungus. Unfortunately That Likely came from your organic soil.
Mature plants can handle real soil and all of the fungus and bacteria that come with it but seedlings cannot. Still lots of time to resow and That is my recommendation. Bleach out all containers and clean your area very well also before resowing.
KarenO
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