Although this is an obvious first step to any mod it is also the most vital. A good plan should consist of accurate measurements, colour schemes and whatever other important information your mod is going to involve.
Writing out a build log is a useful way of keeping track of what you need to do as well as saving you overlooking any essential build details. Another useful tool for more advanced project planners is Google Sketch up or Adobe Illustrator. This software allows users to create 3D "Mock Ups" of projects helping determine end results and measurements with perfect accuracy.
An often overlooked aspect of modifying and using power tools is using the proper safety gear. After working around building sites and carpenters for years I have seen quite a lot of power tool related injuries some of which involved tradesmen with 30 + years of everyday experience.
This being said, use your safety gear, even a one inch cut into the softest material is enough time to mess up and loose a finger. Remember what your mother told you, "your greatest tools are your hands and eyes."
Glasses - $5
Get in the habit of putting these on when you enter your work area, there is nothing worse than cutting or grinding something only to be reminded that you aren't wearing your protective gear when you have a really close "shave".
Safety glasses are inexpensive and easy to find a pair with good safety standard. I own a clear pair and a tinted pair (which are useful for jobs with sparks or bright lights.)
Gloves - $5
Hot surfaces, jagged edges and sharp cuts can lead to some nasty injuries. Grab yourself some lightweight leather gloves. I cannot count the amount of times my gloves have saved my hands from injury.