I agree that picking him up for short periods is a good idea, but not by the scruff, even if you are supporting him. Mother cats don't actually use the scruff, but place their jaws gently around a kits neck. This is possible because of the tinyness of a kitten. Would suggest you pick him up with one hand under his bum and the other holding his body.
Will he allow you to stroke him when he's sitting on his own? If so, do this little and often; if he won't allow this, play the following game:
hold your hand about 18 inches above his head; wriggle your fingers and say, in a quiet, silly tone of voice "he's coming, he's coming, he's coming" etc. While saying this, keep wriggling you fingers and move your hand slowly towards the top of his head. Initially, he'll cringe, but should be curious enough to stay put (keep your voice soft and playful). Eventually, when you get there, tickle the top of his head with your wriggling fingers and say, "he got you!"
If you play this every day, he'll learn that your approaching hand means that he's about to be tickled on top of the head and the cringe will change into him reaching his head towards your hand.
I've done this trick with feral and nervous cats when they've been ready for it. It works, and teaches them to accept stroking.