How good do the headers need to be? If you are trying to grab every last erg of power then you'll need custom headers since none of the factory built headers have a perfect flange. If you are just building a bracket car then factory headers are fine. If you need to custom build headers for fitment reasons then factory style flanges are a decent place to start. If you want to have headers that help the engine make power then the flange and the first few inches of tubing should match the exhaust port exactly. Most off the shelf headers have a large step at the flange which kills velocity at exactly the wrong point. Get that flange correct and you've won a big part of the battle.

If you can have the first few inches of pipe off the head straight then you'll make more power. If you can use large radius bends you'll make more power. One or two step headers will make more power but cost a lot more money and time. I ran 2 inch dyno headers on my race 514 at 900+ hp even though the formula says I could've gone larger. The trick was that they matched the port very well and they were straight off the ports. The TTI headers I have on my Duster make very sharp bends right at the port. Those headers fit in the car but they cost the engine a bunch of power. Of course as Joe Sherman used to say, "I never found any power in the exhaust". Joe had more dyno pulls under his belt than most anyone in the business, header testing rarely finds much power. Power usually just gets lost on the exhaust side.

I've used PipeMax for years. It is a very useful program for a lot of reason other than header design. If you're serious about making power then PipeMax is a good program to have on hand. The cam portion of it is a little odd but the dyno prediction part of it is pretty good. I think it is built on a very solid math model.