Fix uploaded as ver 0.105c Should fix the problems you described.
Let me know if the stockpiles remain stuck at 0, I'm still not quite sure what's preventing that from working, but I did deploy a fix that should make it work (worked in my tests).
Used your suggestion to fix the mine ladders, you now have to activate them to climb up.
crafting lvl not being saved may be due to the plugin reinitilizing everytime you use a crafting station, fixed that.
(Reinitilizing the plugin was to fix another more minor issue, I will be keeping that in mind going forward).
Thanks for pointing out the bugs you found.