Ok, so I didn't get that the first time. Makes sense now.
Still not sure if mounting the gearbox at an angle is a good idea. I'm afraid it will put unnecessary strain on the mounting flanges. I really think it should be mounted flat. How out of kilter was it? It will probably be fine, just would make me nervous.
Interestingly, the parts books don't show the shims on the gearbox, but my QA has them too.