Whoa, this is really awesome. There should be more MC style spriter like you.
I made also a small illustration of what you could improve.
Red: As Nebeshin said, there is this small perspective error.
Green: Another problem is that the bottom of the clock is round, but the top isn't.
In MM the clock was not completely round like you did at the top of the clock.
There was one corner for every hour. However in the artworks the clock was round.
So you could use a clock like in the artworks or like in the game, but at the moment your's looks a little bit like a mix of both.
Blue: I think the transition between the blue highlighted part and the upper clock tower has too much contrast. At the upper part you used a light-gray, at the lower part you used a dark-gray and actually there isn't a real transition between the colors.
Yellow: I agree with Xiphirx. You should you use dithering. Furthermore I would recommend you to use the pattern you used for the the tower also for the top orb. In MM the orb used the design of the walls of the tower.
Anyway, nice work.