Its much harder to litter train a non-neutered male, they often spray urine and poop to mark their territory too. You may find keeping him confined to some extent helps though, at least until he learns where to go. Also most rabbits don’t like being picked up so I wouldn’t worry at all about not being able to pick him up, I still cant pick Bramble up without a massive fight and I have had him since he was six weeks old.

You are doing the right thing by picking up the poop and putting it in the litter tray, do the same with pee (use kitchen towel then put the towel in the litter tray). If you keep him in a smaller space (an x-pen is a great idea) he should learn where he should be going reasonably quickly but as he is un-neutered he may not be 100% toilet trained unless you have him fixed.

As for bonding with your bun, let him come to you. Sit on the floor with him, rabbits prefer to interact on their own level. When he comes to you let him sniff you but don’t touch him at first, let him get comfortable around you then you can start petting him gently. It takes time but it does work.

KIrstyol nailed it. Nothing for me to add. But I’ll try ha ha.

Litter training falls into place once they are neutered, as she said. I’ve heard some buns still like to pee on soft places like beds and couches even after neutering. But def. keep him more confined at this point…like K said