".........What I noticed when I removed them (I have run the car for about 50 miles and it seemed to run great) is that the most rearward cylinder on each header is clearly running ultra lean. ...."
"...... The motor seemed to idle fine......."
OK, so the car is running "great". as described by the OP
additionally, it "....idles fine..."
You don't have a problem. If there was a lean condition so bad it was causing engine damage, the car wouldn't be running great and idling fine. With two cylinders REALLY running extremely lean the idle would be hunting all over the map, and you would be down on power. Just because the carbon residue is lighter colored in the two rear cylinders is not reason to think the sky is falling and something must be done.
You will never get all the cylinders to show the same exact burn color with a Cobra Hi-rise manifold.
So put on your headers when they are done (again) and drive the car. When you have a problem you won't need to be analyzing the inside of the headers to discover it. It will be obvious and manifest itself by an unstable idle, massive bog off idle, and poor acceleration. Until you have those symptoms, you don't have a problem.
Z