First, is there a reason you are so set on doing this? Some birds just don't like some things. Second, is he molting early? Molting can lead to discomfort. One of my green cheeks (a 'pineapple conure' is a green cheeked conure. Green cheeked is the species, pineapple is the color. Pineapple is actually a combination of the yellow sided mutation and the cinnamon mutation) also is snugly but does not allow head scratches, and is very vocal about it, when she is molting. Unfortunately this leads to her pin feathers lasting an extra long time since she is terrified of other birds. We have to be sneaky about it. We lulu he r almost to sleep. She lays on her back in our hands and looks dead. Then we slowly work our way up and gently work on the worst of he pin feathers, but the second we make it uncomfortable, she is wide away and irritated.
If you MUST touch her head, train her to accept it using treats. Use the clicker method, ideally, but be sure you understand exactly how that works before you try it. Touch him for just a second, reward, etc. begin to touch the head for longer periods, to move your fingers a bit, etc, always rewarding. But understand you will just be training him to accept it, not to like it. If you don't have a reason he needs to accept it, then why bother? Also, be careful with the cuddles. I know it is hard with GCCs but watch the hormone triggers! Stay away from his back end, watch for nesting behaviors, etc or you may end up routing your snuggle buddy into a jealous mate.