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1/8 in. angle is a good choice. Make your first header on the car (or at least tack it). Then, use it to make the jig. Next, take a piece of angle and use it to bolt the flange to. Off of that make a frame that you can add more pieces of angle to in some of the long straight pieces of the primary tubing. It will look crazy without a header in the jig, but they work. The size angle depends on primary size. 2 in. is a good size for most. This is a very basic description I know, but it should help.
I guess I think a little different. I would fabricate the exhaust system on the engine/car, then start doing the power and tuning development on it. Lots of cutting up and changes until it works just right for the application. When everything it the way you like, then build a jig from the prototype. Just remember to let the fixture have a little "give" as to not stress the welds durring cooling. Have at it !