So you want a custom guitar?
I didn't start by wanting a custom guitar. I bought and sold a lot of guitars. Every one was different in some way: body style and size, scale length, pickups, vibrato, fret size, neck shape, fretboard radius, woods, construction, ... lots of variations. I played them all; gigged them all. Along the way, I made note of the details that I liked and didn't like. I used that knowledge to guide my next purchase. Over time, that led to one guitar which was almost perfect for me.
I played that guitar almost exclusively for three years while trying to find one that was even closer to what I really wanted. I looked into the custom shops of the name-brand builders and either couldn't get what I wanted (limited by a very narrow set of parameters that they were willing to customize) or found the cost prohibitive.
Eventually my search led me to the smaller builders, and I corresponded with several who seemed capable of building the guitar I wanted. It turned out that the luthier having the greatest breadth and depth of experience in building full-custom instruments (as opposed to simply customizing the details of a few stock designs) was within walking distance of my house.
I arrived at our first meeting with some carefully thought-out requirements as a starting point. We hashed out some additional details over a few sessions, two of which involved reviewing and critiquing a full-scale plan drawing of the guitar. No detail was left to chance, so I knew exactly what I was getting. And every detail was executed exactly the way I wanted - no compromises. The luthier's experience was very important in designing the internal construction of the instrument to make it respond the way I wanted; that's something that you simply can't do by selecting from a checklist of options.
Once all the details were finalized, I signed off on the design. Then I waited... for a long time. There's an amazing amount of work that goes into building a full-custom guitar. The builder is not only creating a guitar, but also the tooling and jigs that are a necessary part of the construction process. Every bit of this guitar was handmade - no CNC. I got status reports every now and then, which was a thoughtful touch. I always responded by saying "Thank you, and take as long as you need." You can't rush perfection.
The end result: I got a guitar that was exactly what I wanted: a highly-refined version of my favorite "off the rack" guitar that I had been already been playing for years.
I have no idea what the resale value would be on this guitar, and I don't care. In the long run, I'll save a lot of money by not trying to find a guitar that's better for me.