I disagree with Russ. There are differences between stock and custom bikes just as there are differences between a custom made suit and a suit off the rack; just as there are differences between a Huffy and a Trek. After being happy with my stock bikes, I decided to invest in a custom bike. My last two bikes have been custom (Waterford) and I can tell the difference in the ride and how I feel at the end of the ride. An added benefit is the very noticeable craftsmanship differences. There are some excellent stock bikes and investing in a custom bike is not necessary to enjoy riding, but there are differences, and that is why there is a difference in cost.
I have a stock Southwick suit that cost a few dollars. I am sure it is far superior to the vast majority of custom suits sold. I also have a stock Waterford. The finest of lugged bikes. Reynolds 753 frame. Silver soldering on the small lugs. Beautiful red paint. Are you implying that Waterford makes good custom frames and crap stock frames? Do you think they use different welders, cutters, painters for the custom and stock frames? The good people make the custom bikes and the worthless people make the stock frames? Odd.
If your body shape requires a custom frame, get one. It will fit you better. Assuming the maker measures you correctly and knows how to design frames. Not a given. But if you are like 99+% of the people and have normal shaped bodies, you don't need custom frames. Stock will fit you perfectly fine.