Cats learn fast. You have to teach them you're trustworthy and won't torment them when you pick them up. Be predictable unless your cat is in play mode. Those kitties that are skittish around people were probably chased, thrown, used for target practice, etc, at one time.
Place him in the litter box a few times. Once they feel the "sand" squish beneath their paws, they will gravitate toward that one place in the house, when the need arises. I lived with a female car for a while and never had to clean up cat waste.
If you feed a cat scraps while at the table, kitteh will hang around during every meal, hoping for a handout. Duh. My cat never got up on tables much, though every now and then I'd reenter the kitchen to find her on a chair back sniffing in the direction of food on the table. I'd yell and unceremoniously shove her off. She'd scamper off to the next room and cower under a chair for a bit. Cats don't necessarily connect your sudden roughness with their transgression, but if you yell and attack them when you find them in some off limits area, they will automatically hop off when you approach, unless they're feeling unduly lazy or it's a long way down.
My cat had a favorite corner of a tweed couch to scratch. Tore it up. But she went outdoors a lot and got to scratch on bare roots in the yard. As long as it was warm, we'd put her outside for the day while we were gone.
Food: Cat probably won't be too enthusiastic about Special Kitty, but he'll eat it. Just buy small sacks of various brands and make a written note of what varieties appeal to him. Purina, Iams are good.
Cats might climb into bed with you. They'll hear you snoring or breathing and they'll want a piece of the action and lay up against you. They can leave plenty of fluff behind, depending on time of year. Might want to pick up a cat brush for loose fluff removal. Cats love being groomed mostly.
I'd imagine females have more of a nesting instinct. My female cat was always trying new spaces. Sometimes in a cupboard, in a closet, under a bed, on the back of the couch, guest bed, top of computer CRT. Anytime a new box appeared on the floor she'd explore it and maybe settle down inside. I think the favorite bedding areas get too dirty after a couple days and that prompts them to seek other niches.
I had problems with my cat climbing onto the warm hood of my car, leaving footprints sometimes and flea debris behind. I charged outside and drove her off every time I caught it. Not sure how to avoid it other than coating my front bumper with vaseline.
Enough kitteh talk, back to work.