When did you get him? He might be shuddering because he’s nervous. The second one seems like a binky. Bunnies do that when they are really, really happy. I don’t know why he was digging, though. Lastly, bunnies only thump when they are scared or annoyed, so he isn’t that scared of you!
If you got him recently, you might want to give him a couple of days. After that, approach him. If he doesn’t run, then sit by him and talk to him gently, pet him, give him treats from your hand. Do this for a while, and when you see he’s more relaxed, start spending more time with him! When you have time, sit in a room with him, maybe read a book do work, anything! Occasionally pet him and give him treats. When you give him treats, make him come on your lap. Sooner or later, he’ll get used to you and come sit on your lap without treats! And then you can progress to picking him up after a while.
That’s pretty much how I bonded with my rabbit. Except on the first day, I wasn’t very experienced and didn’t leave him be. I pet him and didn’t give him the space he needed. So my bunny was very scared on the first day – but I didn’t know that then!
Well, now I know…