Find a time frame you want to complete your guitar in. Putting together a guitar with all stock parts can be done in an afternoon, but custom work can consume a good amount of time. Most of the time spent will be finding parts and having them shipped to you. Find sellers that will send packages out in a timely manner and use fast shipping methods.
Building your own guitar is not a way to save money. Buying one off the shelf is cheaper. This being said, know what you want to build and price everything out. Once you have your price in mind realize it will most likely cost more. Also be sure to look for sellers that combine shipping cost if you purchase multiple items and be sure to ask questions so you do not buy something you do not need or thought was different.
How will you use the guitar? Are you going to play gigs, play at home, or just for display. If you are going to gig a guitar, look at used parts that may not be in mint condition. This way you do not have to go through the traumatic "first scratch" when you are on stage. You will also save a good hunk of money over buying new. If you are building something to hang up on the wall or to be a case queen, you can cut back on what pickups and anything else that you will not see for the most part.
Make sure you have an area that you can lay out your guitar to put together. It needs to be in a location where nothing can happen to it (away from pets, children, etc.). You will also need several tools. A Philips head screwdriver, pliers, wrench, and a soldering iron. These tools are very easy to obtain and very affordable. If you plan on building many guitars, buy a soldering gun to get the job done faster.
Next: Pickguard Installation