I thought the whole body of information of the prior art was fair game to argue. In particular, the result of the combination does not function, because the process taught by reference A.
Karen's right here. The entirety of the reference
is fair game. However, the examiner is free to use only part of the reference.
Whether A teaches a method of manufacture that could not possibly result in a metal B is irrelevant. What's relevant is whether the ordinary artisan would have found it obvious to have used all or part of A and all or part of B to make something that would have infringed your claim at the time you made your invention.
Paraphrasing the essence of the examiner’s response:
…the structure of the claims is taught by the combination, not the process of making……
Further, the examiner says:
“If an arrangement substantially identical to that of the claimed and disclosed invention won’t work as argued by Applicant, a potential 35 USC 112, 1st paragraph operability issue may have arisen as this would imply that the Applicant’s invention does not work as disclosed either.”
What the examiner appears to be saying is that, if your argument is that there's no way to make B out of metal, then you're claiming something that you haven't properly enabled.
Whether the examiner is correct depends on your specification. If a metal B could not have been made using techniques within the ordinary level of skill in the art(s) at the time your invention was made, then you will have had to teach the ordinary artisan how to make one.
The answer in overcoming that sort of rejection is to show that your specification made the impossible possible (at least for the ordinary artisan).
IF.....IF!!! The details of understanding my argument requires visualization of 3D interlocking structure. I'm not sure my response was fully communicated and understood by the examiner, or is there a flaw in my thinking?
Hard to say at this point whether there's an error in your thinking. If you think that the examiner is limited to the particular method of manufacture described in A, then, yes, there's a flaw in your thinking. However, it's entirely fair that you require that the examiner show how a metal B could have been made using only ordinary skill prior to your invention. If you think that how to make a metal B was no mystery (even though it could not be made with the process of A), then that challenge would be pointless.
If there really is some reason that a metal B could not have been made using only ordinary skill until you told the world how to do it, then your thinking may be sound and you'll just have to make that point.
If you think a little show-and-tell with the examiner to explain the 3D modeling complexities, an interview might be worth the effort.
Regards.