Yes, stevesmum, it's best to wait for them to come to you before trying to pick them up. Two of mine were hand raised so they naturally go to the front of the cage to be pet.
Try to shield their cages from direct sunlight. Frozen water bottles tiles and wet clothes are helpful. I have my hutches on a covered porch and keep a fan on to circulate the air.
Try gently holding your hand over his face/eyes. My buns try to jump out of my hands when they know I'm getting ready to put them down. I find they are much calmer when I cover their face.
LOL. I'm a bad Mom. I WASHED bunny blankets the other day. One of my bunnies was quite perturbed. He had to get used to the smell if a clean blanket and rearrange it just the way he likes it. LOL
Are you sure he isn't stomping? When my bunnies stomp it sounds like a popping niise. They do it to scare away predictors or claim their territory or just to get attention.
I have a 36 inch high x pen and one of my buns will climb to the top. I tied using a light colored sheet attached with clothes pins across the top of the pen and he still climbed. Then I tried a dark colored cloth and he stopped climbing. Go figure.
The "pee pads" can be found in pet stores or wherever pet supplies are sold. They are very absorbent and will help with the odor. My baby buns used them in their crates until 8 weeks old and then I gave them a litter box. In my opinion a nine week old bunny should be kept in a confined area...