We got the 42" for Henry when he was 8 weeks, and it was perfect for him.
When we got Katie we bought the next size down, and as she was an adult it seemed too small compared to the one Henry was in.
In the 42", we put his basket at the back of the crate, paper and his water bowl at the front and it was fine. Of an evening we would place a dark sheet over the top so it was nice and dark in it - oh with my dressing gown over the front door - he like pulling the arms through?
He was very good with toilet training, having a larger area to go in didn't seem a problem - he just didn't like doing any mess in it.