@Cait: As far as size goes, it's a simple matter of logic: You got a house that looks two-stacked with an attic (the frontal high windows seem out of place though... you sure they belong there?), and you got a clocktower that looks three-stacked plus attic with a horribly misplaced cellar door ^^ So yeah, in theory, this isn't all senseless, as it might just be a big house... however, your tileset kind of limits you in the way to create single-stacked+attic houses, so yeah... if you want the giganormous tower effect, increase it's size!
In general, VX's shadow is really messing things up for you... try to draw shadows yourself, and disable VX's, as it doesn't work on anything but stiff 90° angles (meaning it sucks for many many tiles).
For your second tower attempt, it's another logical thing to bear in mind: Especially higher buildings need to be supported from underneath, meaning a string tower with a bulky, made-of-stone block on top won't work out too good in real life. I mention this because it's unlikely the tower will crash down in your game by itself, but it's still a very wonky thing to see for the regular people that live in the regular world. That said, as soon as you tell the player why something is like that, it's alright to use it, as you defined ingame logic.
The roof itself looks alright, but what might be bothering you is that it had an edge instead of a tip.
For the recoloring part, as you're apparently using Photoshop (and a very strange method to export images out of it ^^" ), you have a lot of methods up your sleeves to recolor something. The probably easiest and fastest way is through the Hue/Saturation dialog (Ctrl+U), which lets you adjust different values to change your colors, as well as allows you to completely recolor them (by checking the respective checkbox). This is by far not the best, but definately the fastest and easiest method. Feel free to try out some of the other color management tools Photoshop offers you by looking through the Image > Adjustments submenu.
At the end of the day, you want to use your own palettes though, in order to maintain a style throughout your game as well as to tell yourself you did something right. Finetuning sprites that aren't palette-based can be a pain in the ass, however could save your game's appearance in the end. Make sure that at least when you draw sprites, you try to stick with the same color range for the same project!