It may look a bit cheesy, but you can fix the gradient issues by removing the gradient altogether. Example: alien pyramids on Cydonia. You could probably even get away with merely palette-swapping them into the bluemetal you're using.
I know how to fix some of the other glitches, though I feel too lazy to tackle them at the moment. Instead I thought I'd share a tip for one: the door creates a seam which you can see through when you have the pyramid section directly above it. It's the door in this case, not the pyramid piece. If you shift the door texture 2 units to the right, it fixes its position. It should look okay everywhere you put it unless you put it next to other textures that are offset to match. I glanced at the LOFTs and they look fine, so it should be entirely visual.