I will give it a shot at the 40mm/s. I also noted that one of my cut out windows was bumping the tower close to the location where the stagger occurred. It was all brute force, nothing elegant. I will need to do some digging to get my mind around making things a module, and using intersection... =) Love a challenge though, so I will give it a look. Thanks again!
Mike

You know, it looks like some of your layers are more aligned than others. Perhaps turning down the acceleration or just printing it without acceleration (I typically print at 40mm/s - my Replicator can go a lot faster, but this gives me the best results).

I'm not sure if this would help your print at all, but I think you're probably making the design harder than you really need to.

It might work a lot better to design the entire lighthouse as a single object contained within a single module (say, for instance "lighthouse();"). Then, create a module for a cutout, which if subtracted from the single object lighthouse would make one of the colors (say "cutout();"). Then it should be a simple matter of creating one STL from "difference() { lighthouse(); cutout(); }" and another STL from "intersection() { lighthouse(); cutout(); }".

The lighthouse looks great!