I agree with Shorty's message of being a business owner first, tech/mech second, and given I'm primarily a small business owner, and only a hobbyist in a workshop setting, I am going to give you a bit of a business inspired perspective. I will say, if you want to talk more about the business side of things, feel free to shoot me a PM, as I am in the business management business.
First, if you can, answer me the following questions:
1) Do you have any sort of lobby/waiting space?
2) Do you have any specific retail/product sales that you conduct as part of your business? How are those products currently advertised/displayed for your customers?
3) Are you familiar with basic day to day reconciliation, bookkeeping, general business administrative activities?
Onto Organization...
I'll try my best not to duplicate what others have said.
Start with a floor plan of your entire space. measure it out and be sure to plot out the position of stationary (completely immobile objects like lifts and walls) objects that you must work around. Work it out on paper or more ideally CAD software like Sketchup.
Keep your work-space clean, and start with the office. If you are going to continue to work as a one man show for the time being, get your office in shape so that you can maximize your productivity when you are in there. Good habits within the office will begin to spill into the shop as you progress. In addition, DO NOT let grease/shop grime into your office.
Take a good look at your business from the street. Ask family members/friends to drive by or stop and do the same, as they will notice things you don't. Make sure that your clients' first impression (street view) is appealing, clean and well kept. It speaks to the work you do.
Minimize the number of times that clients are in the shop bay, as well as the area to which they are permitted. This is to say, if you are not willing to move the tire machine to the bay door due to it disrupting your workflow, have a cart ready that you can un/load tires for clients right by the door. Better yet, have two.
Throw up a coat of paint while you are working on the shop. White is good in terms of light reflection, but it shows dirt, so keep that in mind. Give the walls a good cleaning and make it look appealing to people.
Tool carts:
Again, I'm just a hobbyist, but keep a tool cart that is set up with the tools you need for specific repeat jobs. You're a TireRack guy, so have a tool cart that is set up with a dedicated set of tools for doing tires. Don't let those tools walk away from that cart. Have another cart for stuff that you take from your main box if you are doing other work near the lift, and maybe a cart for diagnostic tools if you do much of that type of work. Actually if you have the ability, and the volume to warrant it, consider setting up a single bay specifically for those quick in'n'out jobs like tire swaps and whatnot and hiring a second mech to take care of that work while you focus on running the business itself and doing other more intricate or labour intensive work, or vice versa, take over the lighter jobs yourself to free up your time for running the business.