Why spend the outrageous bucks on a Clapton strat and then change parts out?
Seriously dude usually people buy the Artist models because they want to play the same guitar that their hero plays (not my thing but I can see why people do it)

Rather than modding it, I'd sell the Clapton and buy a couple of new guitars to mod.

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"Life is like eating jalapenos. What you do today may burn your arse tomorrow"

I second this! Play around on a MIM Strat. If you get the hang of playing with the controls on the Clapton Strat, it will produce about any sound you are looking for. Leave it stock and let it retain it's value... hacked up signature guitars are a pity!

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Xhefri's Guitars
www.xhefriguitars.com

Ummmm, have you ever worked on a Clapton Strat? It is not just a simple pickup change as there are other factors that can come in with the circuit board, TBX, etc. I know a guy who had little experience with this kind of thing and messed it up, then took it too a tech, who messed it up even worse, and then gutted the guitar and now it has a passive standard Strat wiring. He asked me to put it back to original. Why mess with a Signature guitar loaded with some specialized wiring? It worked for Clapton.....

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Xhefri's Guitars
www.xhefriguitars.com