Actual cost is broken down cleanly in raw material and operations (cuts, bends, welds), so price is very directly a function of design. A mild steel header of production quantities (say order of 50 to 100) would be around the $500 mark. A single, well designed prototype header might cost $600-$800 plus a $500 setup cost (NC programming, fixtures), but price lessens if moved into mass production after jigs are made. Heck, they could probably fab an entire exhaust in a day pretty close to whatever specs you're looking for. You could literally drop your car off in the morning and have a header built and done on the car by the end of the day. If you've got some CAD skills and a little time, you can literally give them a design, and they will make a prototype for you buy hand to spec with quite good accuracy, or you can go in and they'll do it right on the car or whatever device you bring (bikes, karts, industrial machinery). For example, in previous employment I've used Heartthrob Exhaust for a lot of design and fabrication for gas/deisel/LP/NG generators.
There are also companies that will build you a header, heck full exhaust, however you want. Moore Performance was thinking about making one, but I don't think there was enough interest to follow through. However, it apparently takes a year to get one made, lol, also not cheap (+$1000). There's a couple people that have stepped up and made some alternatives. Most people just buy Borla knockoff headers from ebay and call it a day. Stock is just pretty quiet and loud doesn't sound exactly all the great either.