There are lots of articles on here regarding your concerns. I can give some tips but the care sheets and searching the forum will probably be the most helpful for you.
Regarding litter box training, not all hedgies take to it. Just like dogs and housebreaking, some are faster than others to learn it and some just don't do it as consistently as we would like. One of mine only uses his wheel which is great for cleanup and one of them leaves pellets all around. I just clean up the pellets, its part of owning an animal and takes very little time. (I use a tissue and do a quick pick-up of pellets in the morning when grabbing their wheels to be washed)
Regarding bonding, keep it up! You can do it! I believe being consistent and gentle is the key. Just holding them on your lap with a blanket while watching tv helps them get used to your smell and the fact that you aren't there to harm them. They may always startle when first woken up, don't worry about that, just scoop him up gently and cuddle. Or, if he's squirmy, lay on the floor with him in a hedgie-safe room and watch him explore. (I like small-critter playpen panels for this) It doesn't sound like he's a biter, so that is a positive thing. Some hedgehogs take longer than others and just like a dog that was neglected this one may take longer to trust if he wasn't cared for properly previously. Also, like dogs, some never entirely trust again but we have to love them and show them we are trustworthy anyhow. I would give it some more time.
Regarding litter box training, not all hedgies take to it. Just like dogs and housebreaking, some are faster than others to learn it and some just don't do it as consistently as we would like. One of mine only uses his wheel which is great for cleanup and one of them leaves pellets all around. I just clean up the pellets, its part of owning an animal and takes very little time. (I use a tissue and do a quick pick-up of pellets in the morning when grabbing their wheels to be washed)
Regarding bonding, keep it up! You can do it! I believe being consistent and gentle is the key. Just holding them on your lap with a blanket while watching tv helps them get used to your smell and the fact that you aren't there to harm them. They may always startle when first woken up, don't worry about that, just scoop him up gently and cuddle. Or, if he's squirmy, lay on the floor with him in a hedgie-safe room and watch him explore. (I like small-critter playpen panels for this) It doesn't sound like he's a biter, so that is a positive thing. Some hedgehogs take longer than others and just like a dog that was neglected this one may take longer to trust if he wasn't cared for properly previously. Also, like dogs, some never entirely trust again but we have to love them and show them we are trustworthy anyhow. I would give it some more time.