More gold. This sums up my problem quite nicely.
http://www.stahlheaders.com/ports.htm
I talked to AFR today, and the gentleman manning the help desk told me that the basic problem was the 2" header bolt spacing, which doesn't allow enough room to run the bigger exhaust pipes. Makes sense.
One solution which Stahl offers is an adapter plate. It has recessed bolts for the two inch holes, and then gives you larger ports with the 3" spacing that you can weld up your big pipes to. Somewhat fugly, but your other choices are to say forget it and use the old restrictive headers, or have your cylinder heads drilled for 3" spacing.
UPDATE: not as bad as I feared.
A template as described at the stahl headers link. You tap with a ball peen hammer against the edge of the ports and it makes a nice clean cut.
I placed the template on one of the headers. These are "backdraft type" slip fit headers that are in the process of being de-slip fitted. They are about 1 3/4" diameter at the flange.
You can see that there is some blockage along the sides of the port, but top and bottom the header flange hole is pretty close to the cylinder head exhaust port size.
I'm not going to get my boxers twisted up over this.