I personally don't think the perspective is a problem.
On the issue side, first, your palette. It's got a lot of colors (86) but most of them come from the buttons so it's not an issue. You're using pure greys a bunch in the night time; the greys should have blue hue to them given the lighting (the lighting on the tower in general is pretty bright, actually, but eh, whatevs). I didn't change the dark greys which was kinda stupid since those would actually be the ones with the least of their own color information.
You should also use a warm yellow instead of a cool yellow for the Wizard's, it'll probably go better with the blue background.
My main problem with the screen is that you're ignoring a lot of things that make night time lighting interesting, like your tower remains evenly lit and visible even when it gets further away. The only lightsource, barring torches, should be the moon. I made it a bit more interesting by making the side not facing the moon fade in to the sky. You could also make the very left side of the tower dark enough to blend in with the trees, for more realism and ambience.
How does one generally go about detailing and cleaning up this sort of thing? Are there particular techniques to make it look pixel-art-y? I really haven't done this before.
This is probably gonna suck. Large object patterned with bricks of differing sizes
Just start in one area and spread outward, cleaning up and adding detail. Not sure what you mean by giving it a pixel art look, I guess just use hard edges when you can and some subtle dithering.
Disclaimer: I'm tired so this post might be stupid.