(quoted from post at 15:55:06 06/18/14)
have had two of them over the years get toasted by a lighting strike
Proven protection methods start by defining why damage has occurred. Most really do not know which was the incoming path and which was the outgoing path. For example, lightning far down a street could be obtaining a best earth ground incoming on AC mains, through controller, into pump, into earth, then four miles to distant charges.
Or lightning could strike a tree, go down to the pump, out via pump's AC wires, into a household appliance, out to earth via basement concrete floor, and to distant charges.
You only know this much. Lightning has one incoming and another outgoing current path that is passing destrutively through that pump.
Grounding a pump might only make damage easier. Don't ground a victim. Earth the surge. Impedance (ie wire length), not resistance (ie wire thickness), is even important.
If pump electric wire leaves the building somewhere distant from where all other utilities enter, then that could make damage easier. Rarely understood by well drillers is that the AC wire to pump should leave a building and share service entrance earthing also used by AC electric, phone, etc.
Appreciate this 'art'. Determining why a pump is in lightning's path is necessary before implementing a solution. Connecting all three AC electric wires low impedance (ie less than 10 feet) to single point earth ground may be necessary. Connected by a 'whole house' type protector.
A professional technical note demonstrates this 'art'. But may not be obvious without details. For example, it shows two structures (building and tower). Each has its own earth ground. Any connection from one must connect every wire in the cable to earth. Either by a hardwire. Or doing with a protector what a wire would do better.
http://www.erico.com/public/library/fep/technotes/tncr002.pdf
At this point, all you know is the pump is in a path from cloud to earthed charge particles maybe four miles away. Protection is about making a better path so that a current need not use that pump.