1. Thou shalt document thy tear-down with a log book and many digital pictures. It's 2014 - a good high-res point and shoot camera can be had for less than $100. And don't forget to back them up on DVD or in the cloud.
2. Thou shalt invest in the proper Manuals. Specifically, a copy of the Ford Shop Manual for your year, and the original Ford assembly manuals. You can get them from any Mustang parts supplier. The manual is written with such detail and with great pictures that it is a 'must have' item, and worth it at twice the asking price.
3. Thou shalt Bag and Tag with Reckless Abandon. Each component gets a baggie for like hardware and it all goes in its own box, which is then labeled. Sharpies rule, no ink pens here. Think of it as a love letter to your future self. If you aren't reassembling for 5 years, don't think you're going to remember what all this stuff is. We're not getting any younger. DO NOT just throw all your hardware in a bucket and assume you'll figure it out later. That's like hate mail to your future self.
4. Plan a task before starting it. Have an end point in mind and take your time taking pics, notes and and enjoying the process. Don't...rush...
5. Avoid music with more than 140 BPM. This isn't a workout, it's a project. Pace yourself accordingly. Pandora and Songza are my constant companions while working on the car.
6. No TV in the garage. Tivo the game. When I'm in the garage, I'm focused on the car.
7. Use the right tool for the job. Doesn't have to be top quality (except for measuring tools - torque wrenches and like) but it should at least be the right shape. If you find yourself using pliers and prybars for everything, you may be doing it wrong. Invest in a good socket and wrench set. It's amazing how much of this car can be disassembled with just 7/16", 1/2", and 9/16" wrenches.
8. Safety first! Make sure you know how to use a jack safely. Get a nice pair of safety glasses (ANSI Z87.1) at Lowe's or Home Depot for $10 and wear them. Get some ear protection if you're using air tools or angle grinders. Use nitrile gloves when messing with chemicals (plus this keeps you from tracking this mess inside and angering your significant other!)
9. Know when to take a break. Usually once I've set a tool down with more than the necessary force I find it's good to take a moment and go do something else. Take a walk, watch kitten videos on YouTube, anything. Never turn a wrench in anger. Anger leads to hate, and hate leads to the dark side...
10. Learn the differences between 'perfect', 'good', and 'good enough'. I struggle with this one a lot.
11. Just like the lottery, your odds making money on this project are low. Know the value of the condition #1 car of your year and type and budget accordingly.
12. Save your old parts. I get a bit of flak for this one at home because when you take a bunch of parts off a nearly 50-year old car, it can be a bit of an eyesore if they're just out in the open. But when you order that new flux capacitor and it's not quite fitting, you'll need the old one for reference. Don't throw it away if you don't have to. I hide mine in the backyard by the shed so my neighbors don't have to look at my mess.
13. Order parts when you're about to need them, or the sale is so good you'd be a moron to pass it up. This means knowing what you need and then watching for the sale. I don't have room to stockpile every part I'm going to need, and I'm betting most folks don't either. I waited a year for a good sale to buy the sander I wanted.
14. Get a Marti Report (for 1967 and up cars). The Truth is out there. The Marti report will tell you what your car came with from the factory. It's not often you can get real truth for $40. '65 and '66 owners are out of luck here, or if you're an optimist, have more creative license in their builds.
Not an all-inclusive list, but it covers a common set of problems and should keep the wailing and gnashing of teeth down a bit.