Instead of getting a stool, consider getting a sturdy, little upholstered square ottoman-some even have storage inside. We have a small one that is indispensable for using as a step stool, resting feet when lounging, or as an extra chair on the end of the dinette. I wouldn't be without it and because of it's small size (I think it might be around 16"). It can also be tucked under the dinette if need be.
As far as that overhead storage, try going to IKEA-they have these inexpensive nylon collapsible storage containers that divide and safely store and transport my porcelain china dishes and mugs (and everything else, such as spices, cooking utensils, knife holder, etc.). I'm not sure if the picture I included is the exact ones that we have-these look really white and the ones we have are cream. I just know that they are in the IKEA marketplace, are meant for dividing things in drawers and they fold flat. They have a zipper on the bottom that zips to keep them open. If I remember correctly, they are less than $10.
I also used Ikea's Egyptian cotton full-sized bedding (look for the more expensive set...but this is relative as it was only $35) for the bed and I find it fits perfectly and is super soft and smooth. I also bought one of those full-size memory foam mattress pads to custom fit the mattress (by placing the mattress directly on the pad, tracing and then cutting the proper size. The pad makes the bed super comfortable. We use a queen size duvet from West Elm. I didn't include a picture of that as our color scheme is very different in the Signature