Ctrl N sets the weather and that's about all the control over the weather you'll ever have, if the weather could be altered don't you think that there'd be loads of weather mods in the download section?.
As for changing anything to do with the weather in the mission files that's a busted flush as well, the game engine will take over eventually and do what the hell it wants to do, you could change the weather parameters in the scene.dat file but you could end up making a complete bleeding mess of it as well, your choice, good luck.
