The thing I usually forget? To ensure that the page size I'm using is the same in Word, Photoshop and In Design. Otherwise it's almost impossible to get things to align.
Mysteriously this doesn't seem to happen on smaller novels of say 250-300 pages.
The other factor is the choice of cover art. If I open it to mr ARC-readers, they will inevitably pick two different covers. It happened with Artificial, one of the Christina Nott books and now with Secrets. I've rationalised it by having an International cover and a U.S. specific one.