Have you tried using a dowel rod to pick him up from the floor? If he is uncomfortable in the environment he will gladly step up on the dowel rod to get off of the ground. Not as traumatic as toweling. This usually only works if they are on the floor and freaked out. If you were to try to approach with the dowel rod while he is in the cage, for example, it would freak him out.
The advice about sitting by him and letting him get to know you is really good. He needs to be comfortable with your presence so he can trust you. But you also have to get him out of his comfort zone sometimes. That's why someone suggested that you take apart the cage at the top. He won't have that security of the cage and will be more likely to explore. The cage is his security blanket. But don't do it aggressively. You have to read his body language, get him out of his comfort zone, let him get to know you, all while building his trust. Reading body language is so important when training and living with parrots but especially amazons.
Also whomever said it's only been 3 months is right. So dont be so hard on yourself, you are doing great!