Hello and welcome.
Ok, your new bunny is relatively young - only 8 weeks old. He's been used to different surroundings for the last 8 weeks and now he has a completely new surrounding, different smells, sounds, and senses. Whilst you have provided security and warmth and comfort, to him, it's all a huge emotional upheaval. His sleeping area is his security blanket - it's a place where he can feel secure. His thumping is his way of demonstrating his uncertainty of the situation. He's not tuned in yet to the new world you are providing him so every sound, even though it is normal for you, is not for your bunny. So he is unsure and needs some time to adjust.
My advice would be to reasure your bunny - talk to him, stay with him so he can see and smell you. You are going to be his life, his guardian and best friend and he has to give himself time to trust you. I would leave him for tonight, and then spend time tomorrow as much as you can and let him adjust to the new world he is in. Pick him up by all means as long as you feel comfortable with it, and he is comfortable with it. Most rabbits aren't really happy being handled but if you can get him used to it in a slow and gentle way, then great.
Your rabbit has alot to process and he's still quite young and he's also alone so he's going into emotional overload. Perhaps if you can, try to find a suggle toy for him - maybe a small furry rabbit or similar that he can snuggle up with. It may also be worthwhile looking at perhaps a partner for him. he will benefit from a companion and you still have alot of relatively neutral territory so bonding could be helped by that.
I'm sure that my RU friends will bounce on with some more advice but hopefully I've given you a few bits to look at.
Good luck and please put photos on when you get a chance. We love to see the new bunnies. xx