I do not think it comes from the wiring...

My custom made LAG took several months to complete, because the wood had to dry (it guarantees that I'll still be able to play it in 30 years) Actually, the wood was already in stock, but still, the most renowned luthier are known to have some rare or exotic woods in stock (which are becoming scarcer, hence the price)
Then, everything was done by hand. EVERYTHING! So in the price, I had to pay for the guy who put love and dedication and craft in the instrument, everyday for two months (he didn't work on it all day long, because it has to dry and everything...)

Does it make it better than a machine made guitar? Hell, I have played those for years before I could afford this one... And I'll tell you, my tone is now much easier to get. Staight into an amp, and there you go... Before, finding my tone was a never-ending quest...

Anyway, I do believe in the "soul" of an instrument, and my guitar has a soul... I do not think any of my other ones do have a soul... I have bought a very fine Epiphone Archtop, and even though it sounds and plays great, it doesn't have a soul... Sounds weird...But I guess that's how I think...