Transportation is best done with buses, boksi, and lorries. Boksi is some kind of shared taxi, but mini buses are used instead of the normal cars so dominant elsewhere in North Africa. Trains are now only covering parts of the Sudan, and air flights are so few and so popular that booking a seat will seem like trying to get a ticket to a popular rock concert. If you adjust your impatience, travelling is rewarding, people are friendly, and your budget will not crack. Sleeping and eating is all depending on where Sudanese like to travel.
Most places have governmental rest houses, simple hotels, and fast food stalls.
Some few places, Khartoum , Kassala , Wad Medani , and to some extent, Wadi Halfa offer something beyond that. Luxury is only found in Khartoum. The Sudan is simply not a very safe country, but there are extreme differences between different regions. Special attention is not needed in the north and east, nor in the capital area. Travelling here is probably less hazardous concerning crime, than many places in Europe, North America and Asia.