Ummm I'm obviously quite biased so I won't pretend otherwise, but without playing a Kirn in person I can throw up a couple details that might explain why Thorn charges more:
1. CNC precision going into the fret slotting...
2. Less focus on "keeping things 1960" and more focus on modern improvements (IMO).
3. Thorn has a waiting list (many return customers) so if his prices were too low...
4. Customization goes a few steps further, LOTS of finish options, custom-wound (in-house) pickups, choice of many woods and hardware options etc.
5. Thorn's guitar bodies, necks, PARTS (aside from tuners) are ALL built by Ron Thorn and co.
Too many Ron's!!!
I appreciate the time that you took to write this post. 1. Kirn does buy his necks from USACG, but they are still unfinished. Kirn does the nitro finish, fret leveling, and setup, and he makes his own nuts. USACG necks are CNC cut as well.
2. I will admit that Thorn's neck joint is very forward-thinking, unique, and (probably) very time-intensive to fit properly. It's as though the neck is fit as tightly as a set-neck joint would be, PLUS the screws and neck plate are add further for more reinforcement, better surface contact, etc. The string-tree-less headstock is primarily due to having staggered tuners. I had a Fender Deluxe Strat Plus with no string trees as well. It definitely helps out with tuning stability if a trem is used. (Since I'm lusting after a tele, this is a moot point, though I understand it)
3. Definitely agreed. Supply and Demand. It's the basic tenet of Capitalism. I have no problem with him charging what he charges. It's just the little voice in my head that likes to penny pinch that rears it's head.
4. Kirn offers tons of options as well, although I will concede the fact that Kirn doesn't wind his own pickups. I'm assuming the price of both companies' offerings would go up equally depending on what extra options were requested.
5. Although Kirn doesn't build his own necks, he does build his own bodies, pickguards, nuts, and various other guitar parts. He also does the painting of the bodies and necks and all the shielding work.
I didn't say that both companies offerings should be priced the same. I understand how my initial words could have been misconstrued as such. I'm not one of those guys that goes, "Schecter can build a neck-through guitar with an ebony fretboard, mahogany body and neck, binding, and EMG's for $700, why can't Ibanez do it for the same price?," or "Why does a custom Agile cost so much more than a production Agile", or "Why does a custom Jackson cost $4K?" I understand the reasoning behind pricing, especially when it's hand-crafted by a one-man operation. If I had the extra money, that Thorn SoCal C/S with the Tele configuration would be mine! In fact, I would love to own a J.Custom some day, and that production model cost more than these hand-made guitars do!!!
The bottom line is, I suck at guitar (relatively speaking).
I imagine that my sound would suck just as much on the Thorn as it would on the Kirn! Somebody hand me a Mexican Tele! Ok, enough of the self-deprecating humor. I don't really suck that bad... I just hope that you get my point. In the hands of a great guitarist, these types of things matter. I'm just a couple rungs up from that Gibson-owning doctor that we all know. Sorry to offend your bias.
LOL. j/k, dude. Keep on rocking! 
EDIT: P.S. I tried to rep +1 your post, but it won't let me until I spread more rep around "the pool".
