I can't answer all your questions, but I can give you a little to think about - all FE wedge heads have a cast in "thumbprint" ( pictures below ). The "Thumbprint" actually looks like a thumbprint on the deck surface of the head. The thumbprint can be useful to gauge how much a head has already been milled. There is actually a Ford spec on how deep the thumbprint is on a new head ( I don't know it off hand ), but for the purposes here you'll get the idea. Look at the picture of this first head that has only been slightly milled.
Now look at this picture of a different head that has been milled much more, to the point almost all the thumbprint is gone.
There are also Ford FE head blueprint specs where you can reference things like measurement from the deck to certain bolt holes, etc., but my point is - first you should look at the thumbprint of both heads. I'm going to guess that the one head with less cc's was already milled before you got it. I think along with looking to even up the chamber cc's you will also want to look at how close to the same both deck surfaces are milled so as not to have alignment issues . You're on the right track.
I agree with what fekbmax said, now days I wouldn't advise taking off any more material than needed on rare FE parts like heads and intakes. The C6AE-R heads aren't extremely valuable, and we don't know what intake you have, but best to have a plan in place before doing too much cutting. Since you don't have a block in hand right now you'll want to consider that whatever original FE block you come up with ( if that's the plan ) may or may not already have been milled too sometime in it's past and that's something you'll have to take into account.
