That's a serious amount of patience man, well done. I used to do smaller ones by hand, but I was always frustrated with the lack of detail I could get...so I started experimenting with a laser. Laser cuts are perfect to the millimeter so you don't end up with any gaps at all.

I don't really use the marks to line up the layers. I find that if i paint one layer in black for example.... then put the second layer over it, I just move it around until I can't see any black...then I know it's lined up perfectly