A pro can definitely smooth it out a little bit but your clear will be a lot thinner and more prone to non-repairable mishaps, and on an off road F250 (assuming that's what that is), I don't know if you want that. I used to have an 03' F250 and it had a considerable amount of op, and I just let it go because I wanted the durability of a thick cc. If you do decide to get it done, do your homework on who you get to do it and don't try to get it perfectly smooth. Anything smoother than what you have now will make a big difference, so try to keep the clear as thick as possible.
As far as getting it repainted, that is purely up to you but a *perfect* paint job on a truck that size is going to be quite expensive. There are guys around here that would charge $8,000 - $10,000 for a basic one color *perfect* paint job.