with regards to the night time crying, it might be better to have him sleep with you upstairs on your bed maybe, with no pen, and then when he whimpers, take him out straightaway. I found that the puppy slept for as long as it needed to, and only woke when he really needed not from any other sort of distress, because he felt safe and cosy with human company, and it actually helped with the toilet training. then in the day you could acclimitize him to sleep in his crate whenever you are in or out of the house, for set hours, sitting next to him at first to get him used to the crate and pen, and then awake playing for the time when your dad is going to come over, and the same on your days off. if you maximize the time spent with him when you are there and make his sleep time the time when you aren't there on those two days, it might work.
But tbh I wouldn't leave him in his crate overnight downstairs by himself because it will just make things worse. He needs a lot of human interaction the rest of the time if he is going to be by himself for two hours every morning and afternoon.
But my puppy did sleep two hours morning and afternoon - i was able to leave the house at those times by 16 weeks and not worry he was feeling lonely and scared because I knew he was settled, because I ha observed him behaving like that when I was IN the house, in another room.
tbh if you can just get your dad to come for longer or maybe have the puppy with him in his house it will be much better.
The first weeks are a bit of blur toilet training wise, but they get there in the end. I would just be much more concerned about your puppy being lonely and scared and needed interaction. They are like new babies and toddlers, you cannot train that need out of them.