So, I no longer have a main quest in my quest log.
I never received any dialogue or quest log to take care of the spiders. Faustus sent me to get mushrooms (after the miasma ones were retrieved), and that's all he'll talk about now.
I have found the jailer, but cannot go out of the west gate. The guard says, "Not until the jailer has been found", even though I reported to the commander. I have done ever other quest possible without visiting the shore (to find the whistle, larva queen, etc.), and I am left with nothing to do.