It happens. There has to be a wire hanging down to complete a ground path, or the driver has to be unlucky enough to drive into an active bolt. The vehicle itself is very unlikely to attract a bolt by itself, tires and electrical insulation and all.
It is probably going to need a PCM and the least, and a more likely scenario is that every electronic module on the vehicle will need replaced. This is the part where I start recommending a new vehicle.
If you (or the customer) are dead set on fixing this thing though, start with diagnosing the no communication issue as if it was any other vehicle, ignore the fact that it got struck by lightning. Pretend the customer walked out to go to work in the morning and it wouldn't start, and when you got it it wouldn't talk. Given what happened there is a very good chance whatever is causing the no communication issue is also causing the no start issue.