Well, first, I hope your health issues are resolved and you can get back in your shop. Not being in your best health isn't fun at all.
The honest truth is that I'm a slob, so keeping a shop clean is a continuing struggle for me. I'm hoping that I can stay ahead of myself in this one. I'm going out of my way to try to set it up so that everything truly has a place that it goes...I've never really had that before with my tiny work spaces. I have a lot of tools and "stuff" and the need for storage space has always over taken my shop so that anytime I needed to work on something I had to move things first, which is not a good situation for a natural slob.
Rainman, the original plan was to use the entire garage as a workshop, but I also homebrew beer so I need the bar/brewing area/game room, and I need a place to put garden tools, lawnmower, snowblower, garden tractor, bicycles, etc...so a small portion of the building will become a shed. I'm thinking my lumber storage and air compressor will be in there too, and maybe my dust collector.
Here's a picture of what I've done for small powertool organization... got the milk crates for free on Craigslist, right here in my town.