You're probably right "Lightning" with a direct hit. Replace all the known damaged parts then try the pump. If it works you're OK. If not the pump motor will probably have to be replaced. In your area I'd try Noland of Ferguson but keep in mind that almost none of them know nothing about pumps.
When lightning hits directly nothing is going to help however there should be a ground wire running from the control box, fuse box and pressure switch to the well motor case in the well. The well motor case is the best ground, even better than a ground rod.
I live in Virginia Beach!