I recently set my world to be a 48 minute cycle with days being 24 minutes and nights as well. I'm probably going to shorten it, but I was just testing the waters and it seems like at the same time every day it starts to rain and then it stops for a bit and then eventually thunderstorms. Like I said it is happening at the exact same time of day everyday. I was wondering if there is a way to edit the weather. I'm not too smart when it comes to "ticks" in the time cycle, but I can figure it out. I just wasn't sure if weather worked the same way and if there was anything that I could do.

That's odd. The mod doesn't do anything to mess with weather; that's all controlled by Minecraft. It could be by chance that the weather changed at a similar time for multiple days. You can check the weather interval with commands.