It is not hard to make a good box or case for tools or instruments. And you can often improve the usefulness of an existing box by judicious addition of foam or flaps. By foam, I mean closed-cell polyethelene packing, not to be confused with styrofoam. Styrofoam is weak and crumbly; closed-cell LDPE (low-density polyethylene) is tough and durable. I have a socket set where I replaced the vacuformed insert with LDPE nearly 20 years ago. After years and years of use, with hundreds of removals and re-insertions, the foam is still resilient, still grips the tools, and is ready for decades more.
Step 1: Getting Started
What you need: box or case, foam, felt tip marker, art knife, hot-melt glue.
Sometimes needed: cardboard, paint.
Plug the glue gun in so it can heat up while you think.
Closed cell foam is saved from appliance or equipment boxes. LDPE is what you want. It's easy to glue in place, and very easy to cut. If you don't have a single piece of foam big enough to fill a particular area, you can glue smaller pieces up to fit.