Mike, I'm like you as well. I have quite a few machinist tools that my Grandfather had prior to World War II and I like to store them properly. The one thing I found out early on is that there isn't a tool box I could buy that would let me store my tools the way I liked, so went about designing and building my own toolbox. This is the design I came up with. I even made two of these toolboxes...one for my woodworking shop...and this one for work. I really like the layout of them.
I use the angled top section to keep my most used tools within sight, within easy reach, and the angled top really lets me do that. I spent a lot of time arranging the tools so that any one of them could be removed without disturbing the others, and yet still get as many tools organized as I could. This angled top section is on hinges and can be swung up with an area underneath which is where I keep all my combination squares. I don't use mine as much as I use my machinist squares.
Here are a few pictures of my work toolbox. (The G is the insignia for the old Guilford Rail System where I used to work, and the other insignia is for the International Association of Machinists.) As a side note, you might note the double paneled doors. On the railroad we were required to keep a copy of the rule book, and union book on hand at all times. The inside of the doors allowed me to have a pocket where they could be stored.
I have no intention of traveling from birth to the grave in a manicured and well preserved body; but rather I will skid in sideways, totally beat up, completely worn out, utterly exhausted and jump off my tractor and loudly yell, "Wow, this is what it took to feed a nation!"