I would double-check that those are not root mealy bugs. If those white spots are fuzzy/fluffy, that's a big sign. Google photos of root mealy bugs and see if that's similar to what you saw when you pulled the plant out. I seriously doubt you would have mold from 5 minutes of rain. If your plant is infested with root mealy bugs, that could account for a lot of problems. Glad to hear it seems to have grown a few inches, though. Check into that, and if you can't rule out mealy bugs, look up the treatment for root mealy bugs. I'd keep the plant out of the soil for the time being; if you do have bugs, that will be the easiest way to clean it, and if the roots are too wet, being in the dirt certainly won't help. I'm sorry that you are having so much trouble with these; clearly something is going on!

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I wouldn't worry about the soft pup. I'm guessing it's soft because it's dehydrated. You could leave your cutting that big or cut it. I would think cutting it you may get roots faster because (I hope this makes sense) the plant is using energy to keep the big cutting alive. If you cut it then I would think it would use that energy for roots instead of being wasted on keeping the tall cutting alive. I can't explain that well;). You will get roots either way. Just keep out of bright sun and no water till roots.