What's his viv like? If it only opens from the top, that might be part of the issue as they often get freaked out if they see something huge (our hand!) looming down on them from above, it's much easier and less scary to approach them from the side. Also, is he shedding? Shedding makes some dragons very grumpy.
The only thing I can really recommend is to persevere. Ignore any naughty behaviour or struggling and pick him up anyway, and don't let him go until he is calm. If he learns that struggling = being put down, he'll do it more often. When my bf got his latest beardie, the shop owner said he'd been surrendered to them by an owner who didn't have time for him, and hadn't been handled enough so was very very skittish. He didn't like being picked up, he would just about tolerate having his beard touched but would sometimes puff up, and if you touched him anywhere else he'd run away. He bit him once that I'm aware of, and hissed several times. Bf got him out of the viv for just a couple of minutes at a time around ten times a day, and after a couple of weeks he was already showing considerable improvement, then we'd let him roam around the room when we were in there and pick him up to move him if he started knocking stuff off places or whatever, and after a couple more weeks he was completely tame and started to actively seek us out and climb onto the bed when I was napping to sit on me. Now, about 6 months later, you can do pretty much anything to him and he doesn't mind, he doesn't care whatsoever if you mess with his feet or tail, and will scratch at the glass to come out when I walk into the room.
