I find that if I replace instalation of FeynCalc w/ the the beta version, then make the changes that you suggest, that the FeynCalc, Phi, and FeynArts(v. 3.2) all boot correctly (no errors). I then run the QED example, and find that I must replace the line:
amplFC = afc /. DiracTrace -> Tr // Simplify;
amplFC = afc /. MatrixTrace[X__] -> Y[List[X]] /. List -> Dot /. Y -> Tr // Simplify
In order to get the trace performed (with similar subs in the remainder of the notebook).
MMA v. 5.0 is quite pedantic about the integrations, so one must tweak the integrals to get the rest of the calc to go, but everything else looks OK.
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