I've adopted three chinchillas and they are all standoffish to different degrees.
Rocky (I've gradually adopted her, she came to live here full time in March) is the most comfortable with me but does not like scritches. She shows her affection by sitting on my leg for a few seconds during play time or nibbling my nose when I put my face up to the cage. She doesn't bark or show fear, she's just not cuddly.
Candy is active, friendly, an escape artist, TERRIFIED of being picked up, and kacks and sprays me almost every time I take her out. She let me scritch her for a minute last week and I almost fell over from the shock.
GoGo is more mellow, calm when I pick her up for playtime, but runs away if I pay her any attention in the cage.
I only offer treats from my hand. I find a comfy position and wait very quietly until they approach me. Sometimes they don't, and then I come back later. I sit on the floor by the cage and talk very softly to them throughout the evening and early mornings.
Are you taking him out for playtime? I find that very helpful in bonding. How are you doing dustbaths? They usually love those and are more relaxed when they're having them.
Good luck...it does take a lot of time and patience.Maybe the breeder you got him from can give you some advice, too.