Whats the advantages of neck thru? Is it more resonant? Im not worried about access just wanna get the best tone. I suppost putting more neck into the body will make the guitar resonate as a whole better.
neck thru = sustain
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I think neck-thru feels a lot more solid, but of course that's totally subjective.
Quote by MichaelOfCanton
doesnt really matter too much if the neck is set well. its about the same.
Yea but necks usually aren't set all that well. Neck-thru is usually the best
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Quote by Sam_Prillaman
neck thru = sustain
Actually this has been proven many times to be completely wrong, neck-throughs provide less sustain than a setneck or a well made bolt-on join.

And it stands to reason when you think about it. A neck-trhough is basically a setneck, but there's more wood coming in from the neck, so that means more sustain right? Wrong, because to make room for that extra wood from the neck, you have to take wood out of the body. Often, you have to cut the body clear in half and glue it on either side of the neck black. Really with a neck-through, all you're getting is a setneck with even more glue involved to dull the tone!

Then there's the fact if they break, a neck-through is basically screwed, it's often cheaper to buy a whole new guitar than repair a neck-through. Then there's the dynamic response, which is killed by a neck-through.

The one big advantage neck-throughs can have though, is fret access. With a neck-through, the majority of the neck/bopdy join is within the body itself, so there's rarely any need for a big hunk of wood up where the neck meets the body around the higher frets. For people wanting to get maximum fret access (usually for playing fast shred high up on the guitar), nothing beats a neck-through, because for all it's faults, no setneck or bolt-on can hope to match a neck-through's fret access.

For you though, since you said you're not worried about fret access and only care for the tone... setneck would be far better. More sustain, better dynamic response. What would be even better is if you could make a really good bolt-on neck, but sadly a badly made bolt-on join will kill sustain and response even more than a neck-through, so that's risky if you can't be 100% sure you'll get a perfect join.
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Quote by MrFlibble
...Often, you have to cut the body clear in half and glue it on either side of the neck black...
Not often, always.

Neck-thru guitars are just that. The neck runs from headstock to strap button. Anything less is set-thru
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Another aspect often neglected when comparison tests are made is the pickups. More specifically, how they dampen the string oscillations - which is what produces the timbre or tone to begin with.

As MrFlibble states it, set necks and even bolt-ons can have great sustain - if they are made "right". But remember that many bodies are made of multiple pieces of wood today. Therefore the glue joint problems are not just present with thru-neck designs.