HELP: what is this?

[Weezard]

Ok I was thinking about this and I realized that my problems began after I started using Top Fin pH Decrease for aquariums. Could this be the problem?

Dunno, SS.
But lemon juice works OK as a PH down.
Hydro PH downer is usually Phosphoric and citric acids.

Notice that they still have tight shoes.
If you can't transplant immediately, at least cut the bottoms off those cups and "bog" them on some unamended soil. Rockwool, perlite, coco, etc.
I'm guessing that the roots have hit bottom and are coiled in an un-manageable stagnation

What's the PH of the runoff water?

Weeze