It looks as though you did a very thorough troubleshooting procedure and test session to determine all of the obvious problems. Given the situation (and the tendency of hidden problems to reveal themselves at very inconvenient times), I myself would probably have leaned towards replacing his entire system as you described. There's no telling what else might be wrong in there that you might not find till a few days later. Especially where lightening appeared to hit the actual building. Better to replace it all now than have to repeat visits to the client. Looked at this way, most customers should reasonably agree that one visit is better than 10.

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