Managed to get through the whole thing, though I don't think I picked up on several of the rules despite using every hint available. I'm pretty sure I'm just terrible at these kinda of puzzles though.
(for the benefit of avoiding spoilers I've rot13'd these, the Xes are wildcards)
For 0004 I ended up with pKqaKgneKKaf or possibly pKKfvgneKKaf, obviously neither of which are correct. I think by that point though I'd lost the plot thoroughly enough that it wasn't really recoverable anyway :p
Also I guessed 0000, but my decoding only came to KebKfKKq and I don't see which bit of the puzzle I'm misinterpreting. >w>;
Aside from that I just have a couple small quibbles with the UI. "Use the show command to inspect its contents." should probably include the number cause I did just "show" a couple times, assuming the command would take the just decoded sequence from context.