Hello
a lot of bunnies don't necessarily like it when you start trying to clean their home area, as this is theirs... :lol: Is it at all possible to remove the bunnies whilst you are cleaning, and so avoid altogether the rather traumatic moments? If not, it seems that he is a little territorial in his cage, and this can be tricky. Is it a top lifting cage, ie, you open the top and reach down and in? This can cause some conflict as the action of you doing this, can replicate the action of a predator to a rabbit in the wild, so cause the 'fight or flee' behaviour, as the bunny has nowhere to flight, he's just left with the fight.... This can be helped by getting a cage that opens to the front, so you can be level with him, and not towering over him.
Then there is also a quick squirt with water from a waterpistol everytime he is naughty, so he associates his naughtiness with something he doesn't do, it is important that he doesn't associate the unpleasentness with you, as this will do little to assist your relationship. Water is harmless, but they don't particularly like it.... maybe worth a try.
Also, when you are doing things with your bunnies avoid any strong smelling perfume, soap etc, as this can also upset bunnies and make them re-establish territories and hierarchies.
annie