PtWB (author of JSawyer Ultimate) never really recommended using PN with any of his mods, as I recall. He mostly felt they replaced PN. I'm not sure I feel the same, but it's been a long while since I looked at JSU and he's notably dropped the egregious economy overhaul, so it looks like a pretty good mod now. You'll have to decide whether you think it replaces it fully or not on your own, but a lot of mods in F&L might be built around PN (and some of the modules certainly add features JSU don't have at all) so keep that in mind. Dropping a mod mid-playthrough might not be ideal, depending on how script heavy it is. Have you tried the Nevada Skies config in-game? Rains are pretty rare, seeing as it is a desert and all... best rule of thumb is to add, not remove, after starting a game. But you can always try the latter at your own risk.