Partial answer posted as a community wiki:
The dead mouse was a male, numbered A-3352.
The most complete account of the Apollo 17 pocket mouse experiment is provided in Biomedical Results of Apollo (pdf, html). A table in figure 7 specifies some vital statistics of the five flown mice:
Weight (g) Food left
Number start end start end Notes / Behavior at recovery
------ ---------- ---------- ---------------------------------------
A-3326 11.2 9.7 30.0 6.5 female, survived, "in worst condition"
A-3400 10.7 8.6 30.0 16.0 male, survived, "groggy"
A-3305 10.2 9.5 30.0 6.4 male, survived, "in the best condition"
A-3356 10.1 8.9 30.0 17.4 male, survived, "in excellent condition"
A-3352 10.0 7.2 30.0 20.1 male, deceased
The behavior at recovery, as well as a mention of the genders of the mice, is described on pp. 389-391.
It's worth noting that the order A3326, A3400, A3305, A3356 and A3352 is from the heaviest to the lightest initial weight, and that every table and list that I have found (including Wikipedia, Biomedical Results of Apollo, and Apollo 17 Preliminary Science Report) preserves this very particular order.
There's no mention of how the mice were arranged in the tubes. The order described above may or may not be relevant to the order that they were placed in the tubes.
Various experiments were performed on the five mice, and in each case the identity of the mouse is specified by number. Thus, it appears that they had some means of identifying the particular mice. However, I have been unable to find how they were able to tell the mice apart. Perhaps they put markings on the mice, or kept track of which tube they were in, or both.
The dead mouse's name is to be determined.
The NASA scientific sources refer to the mice by number, not name.
It seems that most mentions of the mice's names on the Internet reference Wikipedia (often outright copying its text). In turn, Wikipedia cites a Springer book, which I do not have a copy.
Another source is cited in a CollectSpace forum post:
Thank to those who gave me good tips on this subject, and I've now pinned down the source of those names to an interview conducted with Gene Cernan for the long-defunct "Spaceflight News" (No.7). They were indeed unofficially named Fe, Fi, Fo, Fum and Phooey.
but I am unable to find "Spaceflight News".