Bighorn brought up a good one. A typical modern custom rifle is usually a Remington 700 action with an after-market barrel and stock. Sometimes another factory action is used, but the basic principle is the same: Unless the rifle is put together by some "name" maker, you may have some difficulty getting much more money for it than a synthetic-stocked factory rifle of the same make as the action.
Unless, of course, you get it made in some wildcat cartridge. Then you might not get as much as you would for the same rifle in a factory chambering--and will probably have to include the relatively high-priced dies you bought as well.
A lot of people would be much better off getting their first custom made in a fairly conventional round, in a fairly conventional rifle. These are much easier to sell later when you decide the rifle didn't change your life, but another might.
Find the right gunsmith. A guy who mostly makes "tactical" rifles probably ain't going to make the mountain rifle you want, and vice versa.
Others have already mentioned this, but get every detail in writing, down to rifling twist, barrel shank length, etc.
Over the past 25 years I've had several "custom" gunsmiths offer to build me super-rifles for a discount, and sometimes just the cost of the part. Almost always they built the rifle THEY wanted to build, not what I wanted. They acted like they were listening, but they weren't, and after talking to other people ordered rifles from the same gunsmiths, they usually had the same problems.
Examples: One guy who specialized in tactical rifles promised a "light" .260 Remington. I sent him a Remington 700 short action and got a rifle that weighed almost 8-1/2 pounds before it was scoped. Another guy put a 1-12 twist barrel on a 7x57 (!!!!) because he assumed I'd only be shooting 140-grain bullets. More than one gunsmith has demonstrated that he didn't really understand how to free-float a barrel. One made the length-of-pull 14" because he was under the impression (I don't know how) that I have "long arms."
If the smith doesn't ask about LOP and other details of stock fit, he isn't really a custom gunsmith, just somebody who screws barrels and stocks onto actions. There are a lot of those around.
Entire books have been written on this subject. I have several, but the one I'd usually recommend is SELECTING AND ORDERING A CUSTOM HUNTING RIFLE. It was published by Charlie Sisk but is far from a commercial for his rifles, since he wisely had a bunch of people contribute to it. He published it because he hoped it would save HIM time, preventing having 2-hour phone conversations with his customers once or twice week after they placed their order.
