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I have a hand-built deep translucent red strat made of Warmoth parts, with Dragonfire pickups. It's a swamp ash body with a flamed maple top and a flamed maple neck, and it sounds incredible!
I bought all of the parts from Warmouth with the exception of the electronics and some of the hardware. The company gives complete flexibility so you can get exactly what you want. In my case I simply wanted a Jazz bass in Lake Placid Blue that wasn't a cheap import or an over inflated custom shop model. Once my bass was assembled by a local shop's luthier I got way more than what I expected! This unique Jazz bass had a tone and character all of its own and my Fender's have been collecting dust ever since! If you want a custom guitar consider Warmouth.