I don't remember reading a thread about this before so here it goes. 1.Get some strap the same with as the flanges need to be X 3/8 thick. I used 2" wide strap. 2.Set your stock exhaust manifold on strap and mark holes with transfer punch. 3.Measure where the center of the exhaust port would be and mark center. 4.Drill holes the correct size. Use a hole saw for the middle hole. 5.Cut the flange out of the strap. I used a band saw and cleaned up with a belt sander but could easily be done with a die grinder. 6.Bolt flanges to motor and fabricate the rest of your headers. After tacking the tubes together I unbolted the headers from the motor and bolted them to the exhaust manifold for finish welding. Here's some pics to help make it clearer if only the pictures were clear.
Here's one a did a little while back - it's basically the same approach you used, except I didn't have manifolds to use and instead used the heads. Also I'd reccomend drilling the relief holes - makes using the hole saw WAY easier when you start getting deeper. http://www.jalopyjournal.com/forum/showthread.php?t=84665&highlight=hemirambler