CapZap,
5 - 10 percent? Just a nudge, huh?
I can try, but I don't know if I can make it quite so precise. It might be more in the range of 20 to 40 percent.
The good news is that I have tested changing the file, and at least the game didn't crash. The main effect was an increase in the sound of thunder, but not necessarily many more lightning flashes. It may be that some of the flashes are taking place too far away from the boat to be seen. Unfortunately, lightning flashes in the game don't light up dark clouds as they do in real life.
Since the lightning effect is controlled by the scene.dat file, it will affect the last mod installed in JSGME that uses the scene.dat file. Off the top of my head, I know that GWX, NYGM, M.E.P., and possibly other mods use this file, so you will have to work backwards in your activated mods list and find the last mod to change the scene.dat file. Send a copy of that file to me and I will make the required changes and send it back for you to test.
As I mentioned earlier, I think I can use SH3 Commander to randomly select different versions of this file to produce thunder storms of different intensity, such as mild, moderate, strong, and fierce. The only problem with this solution is every storm on your patrol will have the same intensity until you save, exit, and run SH3 Commander again.