I would give him treats - hand feed everything. Even take a portion of his pellets and hand feed them all. As he's eating, give him some light pets, starting on his head. Gradually he'll associate food with pets.
If you sit on the floor with your shy bunny, does he let you pet him? You mentioned petting him while you're holding him, but I'm curious if he lets you do this while he's free. If he's free and doesn't run away, I would say that he likes it. Most bunnies will leave if they don't like something, not hang around. Does he put his head down on the ground and make himself very flat when you pet him? This is a definite sign of enjoyment. If he huddles up and looks uncomfortable, perhaps he's only submitting out of fear, but I think it's unlikely that he would submit when he could run and hide from you instead. I would keep giving him pets, especially while feeding him.
For your more outgoing bunny, I would work on petting him a lot (doing it with food should help). He's obviously not scared of you, and I think with work he will enjoy petting. It took over 6 months of living with my bun to get him to sit still for petting of any kind. Now after having him for 10 months he enjoys petting probably 50% of the time. It's a gradual process, but he'll never learn to enjoy it if you don't do it. Since he's not afraid of you, you can be a little more outgoing towards him. It's my theory that all buns love to be groomed by a bunny friend, they just have to learn that being groomed (aka petted) by you is as enjoyable as being groomed by another bunny.