When I was at a comp store, we used to see lots of lightning damage....more than once I saw a modem make a whole system lock up..you take the bad modem out and everything was fine.
Maybe just pull out your pci cards one by one and see of the problem goes away when you pull out a certain card etc.
You can also physically look at your motherboard..there are little things on it called "capacitors"
Sometimes when you have a surge, some of the capacitors will "blow"...usually when they do they will bulge out at the top
I found you a picture of a bulged out cap
If you look here ----->
http://www.feistworks.com/3comfix/
the 2nd pic down, the 2nd capacitor from the left...the one that has "470uf" marked on it...you'll notice it is bulged out on the top..normally they are flat...so you can look at your motherboard and see if any of the capacitors are bulged out like that...it is possible to replace them but I have no clue what someone would charge. Plus if they are damaged there could be other damage to the board as well.
JP
JP