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You need a good average sample of all the cylinders in a bank to provide feedback to the computer which will affect all the cylinders of the bank. The Ford computer may change the mixture of all cylinders based on the o2 feedback on one side, even though there are two o2 sensors. I'd look into that before deciding on bung placement. It's better to be a little rich on the poorer flowing side than too lean on the better flowing side.
I will assume your going to run the heated o2s (ie, not 1-wire o2s), so distance from the head is not as important for getting up to temp and in closed loop in a timely manner.

You need a good average sample of all the cylinders in a bank to provide feedback to the computer which will affect all the cylinders of the bank. The Ford computer may change the mixture of all cylinders based on the o2 feedback on one side, even though there are two o2 sensors. I'd look into that before deciding on bung placement. It's better to be a little rich on the poorer flowing side than too lean on the better flowing side.

Hey JD, what if, after running the two diff headers, you found that the left side was rich while the right side was "just right"? Since you can't change the headers while doing your tuning, you could a) change the injectors on the left to a slightly smaller injector. Or 2) better yet, install 2 separate fuel regulators, one for the right and one for left banks.

Then you could balance the two sides under WOT. That is where you'll be running, right?

Think out of the box JD! You, of all people, should be able to do that! You're dissappointing me man