I dont know what you mean, i need more information like where you were exactly, the digivice should work pretty much at all times unless i intentionally disable it.
renas in the kuro zone dont level, they are already balanced around the zone and are fine as is
the crystal is not a cutscene skip it skips almost everything in that particular zone, its used to skip zones its not a quest list that gives out rewards
the crystals blocking your path in the kuro zone give you hits as to what you need to do, just explore and youll find the requirements, they shouldnt be particularly hard to find
slime balls do give the defense buff and heal a little, they are not meant to be major items to be relied on in battle
item numbers are a side effect of a plugin, its not important