I don't know about ideal storage or stacking the parts in the case. I wrap a piece of fabric around cords and pedals when they are stored on the sewing bed.
For the moldy smell, I will eventually air out, I promise, but it can take a long time and bit of effort. All the tricks like , cleaning them with soapy water then vinegar solution, having it out side on a sunny day, keeping the lid open, keep the case and machine in a heated room, keep a pouch of baking soda or heaps of silica bags when closed, replacing them regularly, etc. work. I read of someone who apparently had the worst Featherweight case ever, she just couldn't stand it, her trick was to clean best she could, and sacrificed a few bags of ground coffee now and then. It gradully absorbed the bad smell enough for her to keep the case open in her sewing room. It takes time, I know, the worst usually improves with a good cleaning, within a few days and weeks further improvement, but completely can take years. It will not improve if it packed away and ignored. It's all the regular things we well know that works, we just have to keep it up. I'm thinking we should improve the houses we live in, they should be clean and dry from loft to cellar ;- )