could you try to lift the food bowl up and maybe get a water bottle? there are some food bowls that will clip onto the side of a cage. same with the water if your bunny prefers to drink out of a bowl ( i know mine prefer a water bowl)
i think spaying/neutering a rabbit will also help with the litter box training. also, do you have a high-back litter box with hay lining the front? i found this helped my bunnies to litter box train quite easily. however- sometimes i guess bunnies just do what they want to.
of coarse- it may just be that your bunny is still settling into his new home and is marking everything cause he's so happy it's his! hehe
Anyway, i hope you can find a way to fix the situation. best of luck