40b Lazy Tank

So I just started up a tank after a 4 year hiatus from the hobby. I got a 40b, dirted it with Espoma Organic Potting Mix after baking it in the oven for a little while (dirt was still a bit moist) and then capped it with Eco-Complete and a layer of play sand for future corys (planned on adding them next year). For the driftwood I found a branch of apple tree that had recently been pruned I think? It was covered in lichen and fungi, so I soaked it in a vinegar solution for about a week and a half and got off as much of the crud as I could. I did leave the bark on thinking that the decaying matter would add nutrients to the tank. A few lava rocks were added after being boiled for about an hour so I could affix some needle leaf java.

So here is my problem... I bought 4 ghost shrimp and got a few MTS and put them in my tank last night after it had been running for a few days. I checked this morning and the MTS were not moving and looked dead, so I fished them out and put them in a mason jar with fresh water (we are on well). I could only find 3 shrimp out of the 4, but they are still alive and look relatively normal. I did 2 20%-30% water changes and the shrimp look a bit more active and I've seen them munch on some flake food I threw in.

Do you think there is some kind of toxicity in the tank due to the lichens/fungi or the apple tree sap? I can't imagine it would be the substrate since it is capped. Water params all looked normal for a barely cycling tank and the well water here (Palouse area) is supposed to be really clean and good. Pics included of shrimp and tank.