Captain Drake, would it possible to map both the foreground and background separately? If yes, then I suppose you could simply, for a given stage, place the two sections one beside the others and simply use arrows or numbers to indicate the place where Wario can switch layer.
Of course, since I've never played the game myself and haven't even seen it in action, what I'm suggesting might in practice sound really stupid...
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"With the first link, the chain is forged. The first speech censored, the first thought forbidden, the first freedom denied, chains us all irrevocably." [...] The first time any man's freedom is trodden on, we're all damaged. - Captain Jean-Luc Picard
B*tch, meet reality. Reality, meet b*tch. - Me