I'm sure RT 55J didn't mean to offend. All of us regular mappers take for granted the fact that maps should, whenever possible, be done on a 1:1 pixel ratio. It's most likely that you were playing the game with a 2x display ratio, so each pixel is doubled in size and your emulator takes screenshots of what is actually displayed, not what the emulator emulates.
The available options to correct it are either to play the game at the original size when taking screenshots (though the game might be harder to play at that size), or to reduce either the screen captures or the finished map to half-size (without resampling or using any smoothing features, so that the original pixels which are doubled here go back to their original size).
It looks good so far, though there's still room for some improvements, providing you feel like putting more time on it for aesthetic reasons:
-Parallax scrolling background: This is those backgrounds that don't move at the same speed as the main map. At several points in the underground part, there are sections where the wall is missing and you can see what looks like pipes and "speakers". As you can see on your map, those sections are a bit messy, but there are no magical solutions to correcting them.
The normal way to deal with them is to disable the layer for the background, hoping that it will be replaced by a neutral color that is easily removed (that might not be the case however; if, say, that color is black and the foreground already is full of black, you won't be able to easily remove it). After that, you also take screenshots with the background layer enabled but the sprites and foreground disable to try and capture the background separately. Once you've done that, you can then simply paste the main map over that assembled background so it will show up in the area where you removed the color. This probably sounds really confusing without any images.
Another similar part would be the moving clouds on the surface. The best looking way would be to capture the surface area without the clouds, then capture a screen with the clouds alone, then paste that section several time to cover the length of the level, and then paste the surface over it. In this case, it wouldn't look much different as the differences aren't really visible, but some of use can be really anal about such tiny details. Well, we usually are about our own maps anyway, so don't be afraid of being abused by us for that.
-Animated sprites: Again, this is only a question of preference, but it really looks better when animated sprites are all captured in the same frame. For one example, the rotating fans at the bottom of those tall shafts should look the same way for consistency, as should the captured people.
Hope I didn't scare you
Then again, most of the regulars have been mapping for at least a few years. We've had time to learn and improve.
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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