This guitar is pretty much a mystery, although it is likely that it came out of the Fender Custom Shop on John’s order. It was used extensively during the Heavier Things tour in 2004 [03/12/2004 John Mayer- YouTube], and therefore likely served purely just as of a touring guitar.
By the looks of it, the guitar was based on an early 60s Stratocaster model. It features a rosewood fretboard on a maple neck, most likely an alder body finished in Burgundy Mist, an aged mint-green pickguard, and the standard configuration of three single-coil pickups.
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https://www.youtube.com/watch?v=ajFNKBEui5Q
Here’s another reference