It sounds to be progressing well
I can't pick Raffy (Syrian) up yet. And he jerks around or runs if you try and stroke him on the back/pet him. But I've noticed he doesn't do that if he's eating something! He is so focused on food he will not react at all if I stroke him then. The same when he was trying to climb out of the playpen (hanging on to the top by his front paws). I had to pick him up to lift him down and again he was so focused on trying to escape that he didn't react to me picking him up.
So I think it's psychological. If they're distracted by something they want to do, they aren't scared by being touched.
How do you pick him up? Scooping him from underneath with both hands is best rather than from the top. They feel less threatened like that.