My rabbit caught on to litter training on her own fairly quickly. I would suggest that you make sure your litterbox is large enough for the whole rabbit to sit comfortably inside (not a tiny corner litterbox), and use a different litter in the box than your bedding (if you use bedding. Most rabbits don’t need it). Most rabbits will choose a location to poop and pee on their own. It’s easier to move the litterbox where you notice they do their business most often, rather than to try to change where the rabbit does it. To further encourage this behaviour, keep the litterbox clean, and put hay in it (rabbits often do their business where they eat) or put a hay rack on the cage in such a location that they would have to eat in the litterbox.
As for bonding, you can try hand-feeding different treats. Also, laying on the floor motionless helps to build some trust with them. When I first got my rabbit, she would mostly only visit me when I was on the floor already preoccupied with a book or the laptop. Simple tasks like grooming, feeding, and even cage-cleaning are ways that your rabbit will likely bond with you in the early stages of your relationship. Just be patient, and he’ll be less scared after a while. For me though, it took a year. XD When that happens, you can try training him to do some tricks, which I have found to be a great way to bond.