I like how good these look! Like you said, I think it would be best to combine the maps where possible and use those dots to connect parts that don't fit.
I'd like to make a few comments, most of which are my personal opinion, so feel free to accept or dismiss some of them:
Stage 4: I think the 3rd and 4th sections connect rather well except for a small difference in ceiling height that still looks natural. Also, the bottom-most gear in the 4th section is a bit messed up in its topmost pixels; probably the result of a cut-and-paste.
Stage 5: I think the 2nd and 3rd part would connect very well since they use practically the same stairs except for the colors.
Well, that's mostly it. I'm eager to see the rest
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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