Woah. Hold on there a sec. For some players, in fact a lot of them, Custom Shop isn't really needed. Guitars are guitars and it's pretty easy to get a decent tone at any price point you're comfortable with, but I'd say that Custom Shop can ABSOLUTELY be worth the money for some people (like me). If the OP likes certain specs and colors that aren't readily available (or ever even produced) in any production models. They cost more, but they also hold their value pretty well.
If you just like sunburst, or the more common color finishes and 7.25" or 9.5" neck radii, then I'd say DO NOT go custom unless you realllllly need some specific relicing or whatever. I got mine built to my specs in 2008 and I have never looked back. YES it costs more, but it killed a large portion of my guitar-flipping gas, and I have a really unique and special guitar that is getting better with age. It probably saved me from buying (and selling) at least two or three guitars.
I know we can all do Warmoth partscasters, Danocasters, BiLT, and other custom builders. They can all be cool-- but getting the official brand is pretty schweet. I have never regretted or second-guessed my decision [though plenty have].