I have a friend who wants to build his own guitar. He's going for a sound like that of John Fruciante and Hendrix, but with his own sound to make the guitar unique. I was wondering what the difference is in the body of a Strat and Tele.
tele's are more twangy. and the neck is thicker than the strats. jimi sometimes used a tele neck on a strat body.
Well mainly I wood say the shape. Old tele's (really old) were made of pine. Other than that, nowadays they are both made of alder or ash. To be honest, the shape of 2 guitars that similar in size wouldn't make a difference.
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Both Hendrix and Frusciante use(d) Strats for the most part, but it really depends on what your friend finds more comfortable.

Tele's are just a hunk of wood basically with a cutaway for easy fret access, Strat's are more rounded, have contours, and have a double cutaway for easier fret access. Your friend could make a Nashville Tele, which would be a Tele with a Strat pick-up in the middle, and if they wanted, a Strat pick-up in the neck. It would have access to Strat sounds, but it'd have the signature twang of a Tele. And I'd say they make it out of pine or ash.
I find the Tele has a more rich tone, because it has more wood to it than a Strat.

My dream custom guitar would be an HH an all-mahogany Tele with Stratocaster body contours.
Would you be able to get just a tele body and put strat pickups in it? I've noticed like on ebay, they have tele bodies but it looks as though you can only put tele pickups in it. But idk, I'm not an expert, so you tell me.
hmm i dont think u cud. I have a Tele that I made from a kit and my cousin has a real Fender Tele and u wud have to drill out a bigger hole to fit strat pickups in. (most strats have 3 pickups compared to 2 in a telecaster)

I have a strat and a tele and personally i prefer the sound of the tele and the feel of the strat. if that helps at all....