I had the same inquiry and sought to answer this question via photo documentation.
If you're talking strictly regarding which PJ'd "retail' frame (i.e., the version marketed and/or made available to the public) that Federer actually used in match play, my conclusion is the following:
Federer used the PJ of the retail versions of BOTH the:
1) Wilson Hyper Prostaff (HPS) 6.1 95 with Silver W logo; and
2) Wilson Hyper Prostaff (HPS) 6.0 95 with Yellow W logo.
To be more specific, Federer used the HPS 6.1 95 with Silver W logo over his PS 6.0 85. Federer then used the HPS 6.0 95 with Yellow W logo over his custom 90 frame.
Here are couple photos indicating such:
Wilson HPS 6.1 95 with Silver W logo PJ (over PS 6.0 85)
Wilson HPS 6.0 95 with Yellow W logo PJ (over 90 sq. in. frame)
You can also find some more discussion (as well as visual evidence) of the above from these previous threads/posts:
Hope this helps in answering your question.
Now, what Jimbo has is very special - a PJ of an HPS 6.1 95 with Silver W over an HPS 6.0 95. This unique 95 sq. in. version was not available retail to my knowledge.
On an intersting side, yet related, note, is the fact that Federer never used the HPS 6.1 95 with Yellow W logo PJ on any of his frames. (A bit of background: the HPS 6.1 95 with Yellow logo retail version succeeded the HPS 6.1 95 with Silver W logo version.) Don't ask me why Wilson did this. In any case, I have yet to see a photo of Federer using the HPS 6.1 95 with yellow W, then again, I could be proved wrong as well (Jimbo or Equijet would probably know better.)
Phew! All this is probably confusing, I know. Then again, to some racket heads, including myself, completely lucid - and perhaps a bit obsessive!