Tell us the story of your experience of ordering a custom shop guitar. I am sure all of us have wondered what it was like.
Depends which company you're talking about. Each one is different; Fender you can contact through any dealer and they will bend over backwards to help you, with PRS or Gibson you practically have to be invited by them to have any work done. ESP, PRS and Gibson charge you a small fortune, Fender and Mayones are dirt cheap comparatively, Carvin are either very fair or ridiculously overpriced depending on where you live (USA and Canada: cheap, everywhere else: loldon'tbother). Then you've got some people like TC Ellis offer basically custom builds for dirt-cheap, though of course they aren't quite full Custom Shop quality, at least not in terms of what most people think of as being Custom Shop quality. Some people like Mayones, TC Ellis and Fender will bend over backwards to build you a guitar as close to your dream spec as possible, others like Carvin and PRS give you a few set options and that's it.
Then there are private luthiers or smaller local brands, who are usually cheaper and more accommodating than any big brand, but finding one who's really good can sometimes be a bit of a pain.
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I just yesterday received a guitar built by GMW guitarworks out in California. I'll save picks for a NGD, but it was in general a very pleasant experience. I had played Lee's stuff before and knew he did good work. Then I just went to his website, picked out the specs I wanted, asked him about a few things that weren't on the site (which he went for), and he built it. About 6 months later the guitar showed up. It's very nice.
GMW hot-rod telecaster
GMW soloist
PRS Custom 24
The Illegal Les Paul
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Splawn 4x12

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Gibson and PRS don't really have an easily accessible custom shop. You can get a custom color or a custom pickup configuration from PRS for a small up-charge. The private stock offers you high quality wood and blingblang tops starting at around 10,000. They'll do some body and neck options/customizations but nothing too drastic. I know there are a couple of 7 strings that the custom shop made.

Fender basically has an option list that you can choose from and they'll be very friendly in helping you decide which ones you should pick.

Companies like suhr, anderson, grosh are like Fender except they don't really have any "production level guitars" which are standard guitars that make in large quantities. They'll make a few to send to dealers and such but most of their guitars are one-offs from a set list of body styles/options. They send you an options sheet and you pick the options you want or talk to them about anything that's not on the list. If they can accommodate you they will.

Building a unique guitar with your own specs, own design, etc is a completely different experience. That is all going to depend on the luthier that does the work for you and what he/she is willing to do for you.

I recently ordered a guitar from Anderson. It was pretty painless. I emailed Tom about the guitar they were releasing. Then I called up my local dealer. Then I annoyed him with a bazillion emails about every option on the list. Then I emailed Tom and bugged him a bunch. Then I changed my order about 7 times. Now I'm waiting for my guitar.
Prs se Holcomb is the answer
With everything you guys said so far, would it be wrong for me to say that it would be cheaper and/or easier to just drop 2 grand on a new guitar rather than order a custom guitar?
mr flibble, you said fender will bend over backwards for a custom, as will a jackson? ive seen their custom forms for jacksons and they're extensive, but is that what you mean? also are they pricey, or should i find a good luthier in LA (of course im like an hour from every custom shop, no shit, im an hour or two from corona, im near carvin, my dad drives past schecter's for work every day, etc) or go for a carvin (when i have the money)
i agree with the statements that fender will work with you as much as they can while gibson will not. my guess is PRS is very similar to gibson, but i don't know. gibson charges the price of a house for anything TOO custom and will just plain turn you down if you want any woods that are too exotic. fender usually goes out of their way to find what exactly it is that you want and will work closely with you to build the guitar to your exact specs.

one thing i do know is that the fender custom shop luthiers' names are pretty well known in the custom world, while i couldn't name a single luthier for gibson.
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who are fender's custom shop luthier's that are well known? the only one I know of is John Suhr and he doesn't work there anymore.
Prs se Holcomb is the answer