God permitted Satan to afflict Job severely. The thorn in Paul's flesh was a messenger of Satan to torment him. God permitted Job, the disciples and Paul to be afflicted for their own good, to cleanse their faith of doubt, to look to Him alone for help. Jesus' help is always immediate. The disciples must have fought the rough sea for at least six hours.
Affliction is often long and difficult to endure.
There is no such thing. At death the soul goes either to heaven or hell. It does not wander about. The idea of a ghost shows the disciples' lack of faith. They were insensitive to the loaves of bread.