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Here's a small update.
There was an overwatering issue that caused some problems with some of the plants. I let everything go a few days without any water at all. I just moved nearly all those into a single tray and gave them some cinnamon water. Everything else has been sorted. There were 2 full trays worth of seeds that didn't germinate, but those were really old seeds (3-6 years old in some cases.) I'm really not worried for the squash and cucumber type plants since I have tons of seeds that can be planted in the ground normally. The tomato plants show some stress, but they should even out and be fine now that watering is back on schedule. The pepper plants and tomatillos seem unfazed by everything. Some of the other plants show purplish-reddish hues indicating low water stress.