can't find a way to change how big their clickable area is
The clickable area is determined by the image size. If you want a larger clickable area without making the button larger (as in, "What you see"), make the image bigger by adding an area of transparency around each of the frames in your button image (which will make the overall image larger). You'll need to adjust the positioning accordingly, and you don't want the transparent areas to overlap each other between the buttons on the window - it'll make the mouseover and clicking areas inconsistent.
if you put your cursor on the very top right on a fullscreen window you can't click it and you actually have to move your cursor a pixel to the left
Not sure about that, don't think I've ever played with a skin with the close button tucked all the way into the corner. There is an additional setting for positioning for maximized windows, you might try scooting that to the right a pixel or 2 by reducing the "from the right" number: