Okay folks, here goes nothing.  This is what I have been working on for a bit.  I appriciate the site links, etc.  I even googled more for help.  It is still really hard working at this perspective.  Enjoy and feel free to correct me before its too late.  LOL.

One thing that concerns me with your picture (other than the dark grey beams, which TrevoriuS pointed out) is the red vertical lines on the left-hand side. They are regularly spaced in terms of 2D, but that makes them non-regular in 3D - the ones further away should appear closer together.
There is a useful 'trick' for seeing how this should work - draw a cross on the side of the wall between the corners. You'll see that the point of intersection is not half-way across in terms of pixel count; but it is half-way in 3D (this works because a straight line in 3D is always a straight line when drawn in perspective)
E.g:

Also, Im trying to figure out how to make the ledges, etc pop out.

Just think of them as more cuboids, which you render in the same way as the building itself. Like TreviouS did in his edit, draw lines starting from the vanishing point to make sure you get the directions right.
You might want to try sketching it on paper, so you can see the lines more clearly (if you end up with a lot of construction lines in lo-res pixel work, they tend to become rather messy and unreadable).

Colour edit: (although now I look at it again, I seem to not have made the new colour on the skin quite light enough...)

I'd suggest changing your block shape very slightly to ensure your blocks will tile seamlessly - currently you can see a single pixel of the wrong face along the edge of your blocks when you put them next to one another.
Note that with the shapes I'm using here, there are no visible seams - each pixel is unambiguously on exactly 1 of the 3 visible sides of the block.