you'd have to post one of your greyscale images to be sure but assuming you have the 'building' outlines spaced unevenly placement is going to be problem (I think) so bringing in outlines from illustrator should be the way to go for placement. Extrude those (I don't understand a need for knifing but maybe I don't understand your final result) and do something like in this example...
4581_shadercontrolsheight2.c4d.zip