The toenail that is facing sideways should not be of much concern. If it does not seem that your gecko has any discomfort, I would not worry about it. My 20+ year gecko has a nail or two that face a bit off-center, and as far as I can remember, it was always like that. They do not grip with their digits. It is more or less whatever the nails catch as they swing their feet is how they grip.
As far as the black lump, I would really need to see a picture of it to help you out better. The black lump could be anything from retained shed that has cut off blood supply to that area of the toe to scarring that has occurred due to you forcing shed off of the toe. If you can send me a few clear photos to reptilejoey at gmail, I can further assist you with your issue.