Shop rule #1:Cleanup is the end of every single job, every single time.
Plus you put everything away at the end of each day/shift/work session. No excuses, except in emergencies. In my many years as an engineer and welder, I've met ONE single person who actually worked better with a mess. Lots of people say they work better with a mess, but they are usually fat and lazy, or just useless.
No shame though, getting to that starting line of having everything sorted and organized is a long, uphill battle.
Step one: Overcome nostalgia. I have worked extensively with my father and both my grandfathers. I know nostalgia like no other. I love the most random crappy broken tool with all my heart just because my dad looked at it one time. You have to overcome that. Nostalgia is probably 80-90% an illusion, or a lie in your mind. Take a picture, write a poem, and then throw the junk out. Throw out more than you want to.
Step two. Take EVERYTHING off and out of everywhere, and sort it into categories. If you have a big shop where lots of people work, you'll have to do this in stages, and it's much harder. But a garage, you can do it.
Step three, organize it. Organize everything and use plastic totes, ziploc bags, milk crates, tool boxes, tool boards, whatever. Get it sorted out.
Step four. There is no way to do step three correctly. Once you have it all organized, you will find that 60-80% of it is wrong. That's OK. Now it's cleaned up, and you can handle things one at a time. You don't like how your sockets are sorted? Pull our your sockets and reorganize them. You can fix things one at a time now.