From the description of the problem, it sounds so far as if the thunderstorm may have damaged your router.
Electricity is a funny thing sometimes, and if it hit your cable modem, travelled down the cable and to your router, it could have damaged only a select port or two.
The port you describe that you switched the laptop with the PC - does the VPN connection and all the network applications you use work on all that physical port with other computers?
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"You looked at me as if I was eating runny eggs in slow motion." - Gord Downie of The Tragically Hip
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