Even if you own your own tools, unless you have a great deal of experience you are highly unlikely to save any money. Even on the initial build, it is difficult to save much money, and then there is an additional issue with resale value. Even if you use very high end parts, such as Warmoth or USA Custom Guitars, people are still not going to be willing to spend much money on your amateur build. With a parts guitar, you can frequently get more money for the parts than the whole guitar. And if you build the whole thing yourself from scratch, the resale situation gets even worse.
Now, don't get the impression that I am suggesting that building a guitar is not a good idea. I think it is a great idea. It is a great learning experience, and it is fun, but you should be aware of all the issues involved. You will not save money, and it is difficult to get a guitar which is as good as a factory made guitar, but if you look at it primarily as a learning and recreational experience, then you are going about it the right way, and can have a great experience.
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"Cowards can never be moral."
M.K. Gandhi