First of all, your pony needs to see a farrier more often than once every 6 months. Try once every 6 weeks. He could be sore for any number of reasons, which I won't even hazard a guess at without more information. Hopefully, the lack of early care has not caused any permanent damage, but it will likely take a long time to get his hooves in good health / form.
Why the farrier wouldn't take everything off 6 months ago, but now all of a sudden would is odd. A horse shouldn't be lame or sore after a trim. Generally speaking, if that is the case, the trim is incorrect. But, without having more information, I wouldn't bet my life on that.
If the pony is sore, I would not do more than care for him until I know why he is sore. He is likely stubborn on the lead because he associates it with pain.
Please post pictures of his feet as well as the entire pony standing square to help us to help you help your pony :) If you have pictures of him when you first got him, that might tell us more about why the farrier made the decisions he made as well.