Honestly, for a plain-vanilla build (i.e., no exotic lumber or top-shelf parts), I look at what an off-the-shelf guitar of the same type goes for, and go with that. For a fancy one, get ready to experience a burning sensation, because buddy, the market doesn't care what you paid for a fancy part.
As a hobbyist, I don't expect ever to recover the cost of my time (which, in my actual profession, I can bill at $200-$300/hour), since I don't actually have cred as a builder. Parts markup? If I'm selling a guitar and emphasizing that it's made of Warmoth parts, it is by definition not a factory guitar, but instead a partscaster. Nobody pays top dollar for a partscaster. If you want to make money at this, the name of the game is VOLUME or else special-order work where you're getting paid time-and-materials, with materials marked up to whatever your customer will endure. If you're just looking to shed some gear, part it out or expect to take a net loss.